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ab70551  (Cell Signaling Technology Inc)


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    Structured Review

    Cell Signaling Technology Inc ab70551
    Ab70551, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 93/100, based on 35 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/ab70551/c-Rel+Rabbit+mAb/pmc09278407__mmc2-532-21-27
    Average 93 stars, based on 35 article reviews
    ab70551 - by Bioz Stars, 2026-09
    93/100 stars

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    Related Articles

    Virus:

    Article Title: Structure and regulation of the nuclear exosome targeting complex guides RNA substrates to the exosome
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-FLAG M2 Sigma-Aldrich Cat# F1804; RRID: AB_262044 Rabbit polyclonal anti-MTR4 (SKIV2L2) Abcam Cat# ab70551; RRID: AB_1270701 Rabbit monoclonal anti-MYC Cell Signaling Cat# 2278; RRID: AB_490778 Mouse monoclonal anti-MYC Abcam Cat# ab32; RRID:AB_303599 Rabbit polyclonal anti-RBM7 Sigma-Aldrich Cat# HPA013993; RRID:AB_1856137 Rabbit polyclonal anti-ALPHA-TUBULIN Rockland Cat# 600-401-880, RRID:AB_2137000 Bacterial and virus strains BL21 Star (DE3) pRARE E.coli strain EMBL Heidelberg Core Facility N/A Chemicals, peptides, and recombinant proteins H. sapiens MTR4 Lingaraju et al. (2019a); this paper N/A H. sapiens ZCCHC8 Falk et al. (2016), Puno and Lima (2018); this paper N/A H. sapiens RBM7 Falk et al. (2016); this paper N/A H. sapiens EXO10-MPP6-RRP6N-RRP47 Gerlach et al. (2018) N/A T4 DNA polymerase NEB NEB M0203L T1 RNase Thermo Fisher EN0541 Benzonase Merck 71206 3C Prescission protease MPIB core facility N/A Sup2 SUMO protease MPIB core facility N/A ATP, CTP, GTP, UTP Jena Bioscience NU-1010 – 1013 UTP [⍺-32P] Hartmann Analytic FP-210 Indole-3-acetic acid sodium salt (IAA) Sigma-Aldrich I5148-10G Trizol Thermo Fisher 15596026 phenol:chloroform:isoamyl alcohol (25:24:1) Thermo Fisher 15593031 n-octyl-ß-D-glucoside Sigma-Aldrich 850511P AMPPNP Jena Bioscience NU-407-10 BS3 (bis(sulfosuccinimidyl)suberate) Thermo Fisher A39266 Critical commercial assays Phusion Flash High-Fidelity PCR Master Mix Thermo Fisher F548S QIA prep Spin Miniprep Kit Qiagen 27104 Wizard SV Gel and PCR Clean-up system Promega A9282 TURBO DNase kit Thermo Fisher AM2238 SuperScript III Reverse Transcriptase Thermo Fisher 1808044 Platinum SYBR Green qPCR SuperMix Thermo Fisher 11733046 Ribolock RNase Inhibitor Thermo Fisher EO0381 RiboCop rRNA Depletion kit Lexogen GmbH 037.96 Protein G Dynabeads Thermo Fisher 10009D Lipofectamine 3000 Transfection Reagent Thermo Fisher L300001 Viafect Transfection Reagent Promega E4981 NEBuilder HiFi DNA Assembly cloning kit NEB E5520S GeneJET PCR Purification Kit Thermo Fisher K0701 (Continued on next page) Molecular Cell 82, 2505–2518.e1–e7, July 7, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data NEXTS overall reconstruction This paper EMDB: 14510 PDB: 7Z4Y NEXTS dimerization module This paper EMDB: 14511 PDB: 7Z4Z NEXTL single protomer This paper EMDB: 14514 NEXTL focused on MTR4 This paper EMDB: 14513 PDB: 7Z52 NEXTS with nuclear exosome This paper EMDB: 14515 Raw and analyzed data This paper Mendeley doi: https://doi.org/10.17632/ m5pg349jth.1 Experimental models: Cell lines HeLa:TIR1 Prof. Edouard Bertrand N/A HeLa:TIR1 ZCCHC8-3F-mAID This study N/A HeLa:TIR1 ZCCHC8-3F-mAID MYCZCCHC81-707 This study N/A HeLa:TIR1 ZCCHC8-3F-mAID MYCZCCHC8177-707 This study N/A Oligonucleotides sgRNA oligonucleotides See Table S2 N/A RT-qPCR oligonucleotides See Table S3 N/A RNA U20 ELLA Biotech N/A RNA CUACCCCGAGAGGGGUAG-U60 ELLA Biotech N/A Recombinant DNA pGCT[hZCCHC8-3F-mAID] HYG This study N/A pGCT[hZCCHC8-3F-mAID] NEO This study N/A pBAC[MYC-hZCCHC8_1-707] BLAST This study N/A pBAC[MYC-hZCCHC8_177-707] BLAST This study N/A pEC-Kan-His-GST-3C-hMTR4(FL) This study N/A pEC-Kan-His-GST-3C-hZCCHC8(41-337) Falk et al. (2016) N/A pEC-Kan-His-GST-3C-hZCCHC8(177-337) This study N/A pEC-Kan-His-GST-3C-hZCCHC8(187-337) This study N/A pEC-Kan-His-GST-3C-hZCCHC8(659707)-TRX This study N/A pEC-Strep-His-Ztag-3C-hRBM7(1-98) Falk et al. (2016) N/A pEC-Kan-His-SUMO-hZCCHC8(D416-506) Adapted from Puno and Lima (2018) N/A pEC-Amp-His-SUMO-hRBM7(1-98) This study N/A Software and algorithms ImageJ (v1.51) Schneider et al. (2012) https://imagej.nih.gov/ij/ AriaMx (v1.71) Agilent https://www.agilent.com/ Graphpad Prism (9.0.0) Graphpad https://www.graphpad.com/scientific- software/prism/ AlphaFold Jumper et al. (2021) https://alphafold.ebi.ac.uk/ AlphaFold_advanced Google Colab notebook Mirdita et al. (2021) https://colab.research.google.com/github/ sokrypton/ColabFold/blob/main/beta/ AlphaFold2_advanced.ipynb SerialEM Schorb et al. (2019) https://bio3d.colorado.edu/SerialEM/ Focus Biyani et al. (2017) https://www.focus-em.org MotionCor2 Zheng et al. (2017) https://msg.ucsf.edu/em/ software/ motioncor2.html (Continued on next page) ll OPEN ACCESS Article e2 Molecular Cell 82, 2505–2518.e1–e7, July 7, 2022

    Recombinant:

    Article Title: Structure and regulation of the nuclear exosome targeting complex guides RNA substrates to the exosome
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-FLAG M2 Sigma-Aldrich Cat# F1804; RRID: AB_262044 Rabbit polyclonal anti-MTR4 (SKIV2L2) Abcam Cat# ab70551; RRID: AB_1270701 Rabbit monoclonal anti-MYC Cell Signaling Cat# 2278; RRID: AB_490778 Mouse monoclonal anti-MYC Abcam Cat# ab32; RRID:AB_303599 Rabbit polyclonal anti-RBM7 Sigma-Aldrich Cat# HPA013993; RRID:AB_1856137 Rabbit polyclonal anti-ALPHA-TUBULIN Rockland Cat# 600-401-880, RRID:AB_2137000 Bacterial and virus strains BL21 Star (DE3) pRARE E.coli strain EMBL Heidelberg Core Facility N/A Chemicals, peptides, and recombinant proteins H. sapiens MTR4 Lingaraju et al. (2019a); this paper N/A H. sapiens ZCCHC8 Falk et al. (2016), Puno and Lima (2018); this paper N/A H. sapiens RBM7 Falk et al. (2016); this paper N/A H. sapiens EXO10-MPP6-RRP6N-RRP47 Gerlach et al. (2018) N/A T4 DNA polymerase NEB NEB M0203L T1 RNase Thermo Fisher EN0541 Benzonase Merck 71206 3C Prescission protease MPIB core facility N/A Sup2 SUMO protease MPIB core facility N/A ATP, CTP, GTP, UTP Jena Bioscience NU-1010 – 1013 UTP [⍺-32P] Hartmann Analytic FP-210 Indole-3-acetic acid sodium salt (IAA) Sigma-Aldrich I5148-10G Trizol Thermo Fisher 15596026 phenol:chloroform:isoamyl alcohol (25:24:1) Thermo Fisher 15593031 n-octyl-ß-D-glucoside Sigma-Aldrich 850511P AMPPNP Jena Bioscience NU-407-10 BS3 (bis(sulfosuccinimidyl)suberate) Thermo Fisher A39266 Critical commercial assays Phusion Flash High-Fidelity PCR Master Mix Thermo Fisher F548S QIA prep Spin Miniprep Kit Qiagen 27104 Wizard SV Gel and PCR Clean-up system Promega A9282 TURBO DNase kit Thermo Fisher AM2238 SuperScript III Reverse Transcriptase Thermo Fisher 1808044 Platinum SYBR Green qPCR SuperMix Thermo Fisher 11733046 Ribolock RNase Inhibitor Thermo Fisher EO0381 RiboCop rRNA Depletion kit Lexogen GmbH 037.96 Protein G Dynabeads Thermo Fisher 10009D Lipofectamine 3000 Transfection Reagent Thermo Fisher L300001 Viafect Transfection Reagent Promega E4981 NEBuilder HiFi DNA Assembly cloning kit NEB E5520S GeneJET PCR Purification Kit Thermo Fisher K0701 (Continued on next page) Molecular Cell 82, 2505–2518.e1–e7, July 7, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data NEXTS overall reconstruction This paper EMDB: 14510 PDB: 7Z4Y NEXTS dimerization module This paper EMDB: 14511 PDB: 7Z4Z NEXTL single protomer This paper EMDB: 14514 NEXTL focused on MTR4 This paper EMDB: 14513 PDB: 7Z52 NEXTS with nuclear exosome This paper EMDB: 14515 Raw and analyzed data This paper Mendeley doi: https://doi.org/10.17632/ m5pg349jth.1 Experimental models: Cell lines HeLa:TIR1 Prof. Edouard Bertrand N/A HeLa:TIR1 ZCCHC8-3F-mAID This study N/A HeLa:TIR1 ZCCHC8-3F-mAID MYCZCCHC81-707 This study N/A HeLa:TIR1 ZCCHC8-3F-mAID MYCZCCHC8177-707 This study N/A Oligonucleotides sgRNA oligonucleotides See Table S2 N/A RT-qPCR oligonucleotides See Table S3 N/A RNA U20 ELLA Biotech N/A RNA CUACCCCGAGAGGGGUAG-U60 ELLA Biotech N/A Recombinant DNA pGCT[hZCCHC8-3F-mAID] HYG This study N/A pGCT[hZCCHC8-3F-mAID] NEO This study N/A pBAC[MYC-hZCCHC8_1-707] BLAST This study N/A pBAC[MYC-hZCCHC8_177-707] BLAST This study N/A pEC-Kan-His-GST-3C-hMTR4(FL) This study N/A pEC-Kan-His-GST-3C-hZCCHC8(41-337) Falk et al. (2016) N/A pEC-Kan-His-GST-3C-hZCCHC8(177-337) This study N/A pEC-Kan-His-GST-3C-hZCCHC8(187-337) This study N/A pEC-Kan-His-GST-3C-hZCCHC8(659707)-TRX This study N/A pEC-Strep-His-Ztag-3C-hRBM7(1-98) Falk et al. (2016) N/A pEC-Kan-His-SUMO-hZCCHC8(D416-506) Adapted from Puno and Lima (2018) N/A pEC-Amp-His-SUMO-hRBM7(1-98) This study N/A Software and algorithms ImageJ (v1.51) Schneider et al. (2012) https://imagej.nih.gov/ij/ AriaMx (v1.71) Agilent https://www.agilent.com/ Graphpad Prism (9.0.0) Graphpad https://www.graphpad.com/scientific- software/prism/ AlphaFold Jumper et al. (2021) https://alphafold.ebi.ac.uk/ AlphaFold_advanced Google Colab notebook Mirdita et al. (2021) https://colab.research.google.com/github/ sokrypton/ColabFold/blob/main/beta/ AlphaFold2_advanced.ipynb SerialEM Schorb et al. (2019) https://bio3d.colorado.edu/SerialEM/ Focus Biyani et al. (2017) https://www.focus-em.org MotionCor2 Zheng et al. (2017) https://msg.ucsf.edu/em/ software/ motioncor2.html (Continued on next page) ll OPEN ACCESS Article e2 Molecular Cell 82, 2505–2518.e1–e7, July 7, 2022

    Polymerase Chain Reaction:

    Article Title: Structure and regulation of the nuclear exosome targeting complex guides RNA substrates to the exosome
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-FLAG M2 Sigma-Aldrich Cat# F1804; RRID: AB_262044 Rabbit polyclonal anti-MTR4 (SKIV2L2) Abcam Cat# ab70551; RRID: AB_1270701 Rabbit monoclonal anti-MYC Cell Signaling Cat# 2278; RRID: AB_490778 Mouse monoclonal anti-MYC Abcam Cat# ab32; RRID:AB_303599 Rabbit polyclonal anti-RBM7 Sigma-Aldrich Cat# HPA013993; RRID:AB_1856137 Rabbit polyclonal anti-ALPHA-TUBULIN Rockland Cat# 600-401-880, RRID:AB_2137000 Bacterial and virus strains BL21 Star (DE3) pRARE E.coli strain EMBL Heidelberg Core Facility N/A Chemicals, peptides, and recombinant proteins H. sapiens MTR4 Lingaraju et al. (2019a); this paper N/A H. sapiens ZCCHC8 Falk et al. (2016), Puno and Lima (2018); this paper N/A H. sapiens RBM7 Falk et al. (2016); this paper N/A H. sapiens EXO10-MPP6-RRP6N-RRP47 Gerlach et al. (2018) N/A T4 DNA polymerase NEB NEB M0203L T1 RNase Thermo Fisher EN0541 Benzonase Merck 71206 3C Prescission protease MPIB core facility N/A Sup2 SUMO protease MPIB core facility N/A ATP, CTP, GTP, UTP Jena Bioscience NU-1010 – 1013 UTP [⍺-32P] Hartmann Analytic FP-210 Indole-3-acetic acid sodium salt (IAA) Sigma-Aldrich I5148-10G Trizol Thermo Fisher 15596026 phenol:chloroform:isoamyl alcohol (25:24:1) Thermo Fisher 15593031 n-octyl-ß-D-glucoside Sigma-Aldrich 850511P AMPPNP Jena Bioscience NU-407-10 BS3 (bis(sulfosuccinimidyl)suberate) Thermo Fisher A39266 Critical commercial assays Phusion Flash High-Fidelity PCR Master Mix Thermo Fisher F548S QIA prep Spin Miniprep Kit Qiagen 27104 Wizard SV Gel and PCR Clean-up system Promega A9282 TURBO DNase kit Thermo Fisher AM2238 SuperScript III Reverse Transcriptase Thermo Fisher 1808044 Platinum SYBR Green qPCR SuperMix Thermo Fisher 11733046 Ribolock RNase Inhibitor Thermo Fisher EO0381 RiboCop rRNA Depletion kit Lexogen GmbH 037.96 Protein G Dynabeads Thermo Fisher 10009D Lipofectamine 3000 Transfection Reagent Thermo Fisher L300001 Viafect Transfection Reagent Promega E4981 NEBuilder HiFi DNA Assembly cloning kit NEB E5520S GeneJET PCR Purification Kit Thermo Fisher K0701 (Continued on next page) Molecular Cell 82, 2505–2518.e1–e7, July 7, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data NEXTS overall reconstruction This paper EMDB: 14510 PDB: 7Z4Y NEXTS dimerization module This paper EMDB: 14511 PDB: 7Z4Z NEXTL single protomer This paper EMDB: 14514 NEXTL focused on MTR4 This paper EMDB: 14513 PDB: 7Z52 NEXTS with nuclear exosome This paper EMDB: 14515 Raw and analyzed data This paper Mendeley doi: https://doi.org/10.17632/ m5pg349jth.1 Experimental models: Cell lines HeLa:TIR1 Prof. Edouard Bertrand N/A HeLa:TIR1 ZCCHC8-3F-mAID This study N/A HeLa:TIR1 ZCCHC8-3F-mAID MYCZCCHC81-707 This study N/A HeLa:TIR1 ZCCHC8-3F-mAID MYCZCCHC8177-707 This study N/A Oligonucleotides sgRNA oligonucleotides See Table S2 N/A RT-qPCR oligonucleotides See Table S3 N/A RNA U20 ELLA Biotech N/A RNA CUACCCCGAGAGGGGUAG-U60 ELLA Biotech N/A Recombinant DNA pGCT[hZCCHC8-3F-mAID] HYG This study N/A pGCT[hZCCHC8-3F-mAID] NEO This study N/A pBAC[MYC-hZCCHC8_1-707] BLAST This study N/A pBAC[MYC-hZCCHC8_177-707] BLAST This study N/A pEC-Kan-His-GST-3C-hMTR4(FL) This study N/A pEC-Kan-His-GST-3C-hZCCHC8(41-337) Falk et al. (2016) N/A pEC-Kan-His-GST-3C-hZCCHC8(177-337) This study N/A pEC-Kan-His-GST-3C-hZCCHC8(187-337) This study N/A pEC-Kan-His-GST-3C-hZCCHC8(659707)-TRX This study N/A pEC-Strep-His-Ztag-3C-hRBM7(1-98) Falk et al. (2016) N/A pEC-Kan-His-SUMO-hZCCHC8(D416-506) Adapted from Puno and Lima (2018) N/A pEC-Amp-His-SUMO-hRBM7(1-98) This study N/A Software and algorithms ImageJ (v1.51) Schneider et al. (2012) https://imagej.nih.gov/ij/ AriaMx (v1.71) Agilent https://www.agilent.com/ Graphpad Prism (9.0.0) Graphpad https://www.graphpad.com/scientific- software/prism/ AlphaFold Jumper et al. (2021) https://alphafold.ebi.ac.uk/ AlphaFold_advanced Google Colab notebook Mirdita et al. (2021) https://colab.research.google.com/github/ sokrypton/ColabFold/blob/main/beta/ AlphaFold2_advanced.ipynb SerialEM Schorb et al. (2019) https://bio3d.colorado.edu/SerialEM/ Focus Biyani et al. (2017) https://www.focus-em.org MotionCor2 Zheng et al. (2017) https://msg.ucsf.edu/em/ software/ motioncor2.html (Continued on next page) ll OPEN ACCESS Article e2 Molecular Cell 82, 2505–2518.e1–e7, July 7, 2022

    Reverse Transcription:

    Article Title: Structure and regulation of the nuclear exosome targeting complex guides RNA substrates to the exosome
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-FLAG M2 Sigma-Aldrich Cat# F1804; RRID: AB_262044 Rabbit polyclonal anti-MTR4 (SKIV2L2) Abcam Cat# ab70551; RRID: AB_1270701 Rabbit monoclonal anti-MYC Cell Signaling Cat# 2278; RRID: AB_490778 Mouse monoclonal anti-MYC Abcam Cat# ab32; RRID:AB_303599 Rabbit polyclonal anti-RBM7 Sigma-Aldrich Cat# HPA013993; RRID:AB_1856137 Rabbit polyclonal anti-ALPHA-TUBULIN Rockland Cat# 600-401-880, RRID:AB_2137000 Bacterial and virus strains BL21 Star (DE3) pRARE E.coli strain EMBL Heidelberg Core Facility N/A Chemicals, peptides, and recombinant proteins H. sapiens MTR4 Lingaraju et al. (2019a); this paper N/A H. sapiens ZCCHC8 Falk et al. (2016), Puno and Lima (2018); this paper N/A H. sapiens RBM7 Falk et al. (2016); this paper N/A H. sapiens EXO10-MPP6-RRP6N-RRP47 Gerlach et al. (2018) N/A T4 DNA polymerase NEB NEB M0203L T1 RNase Thermo Fisher EN0541 Benzonase Merck 71206 3C Prescission protease MPIB core facility N/A Sup2 SUMO protease MPIB core facility N/A ATP, CTP, GTP, UTP Jena Bioscience NU-1010 – 1013 UTP [⍺-32P] Hartmann Analytic FP-210 Indole-3-acetic acid sodium salt (IAA) Sigma-Aldrich I5148-10G Trizol Thermo Fisher 15596026 phenol:chloroform:isoamyl alcohol (25:24:1) Thermo Fisher 15593031 n-octyl-ß-D-glucoside Sigma-Aldrich 850511P AMPPNP Jena Bioscience NU-407-10 BS3 (bis(sulfosuccinimidyl)suberate) Thermo Fisher A39266 Critical commercial assays Phusion Flash High-Fidelity PCR Master Mix Thermo Fisher F548S QIA prep Spin Miniprep Kit Qiagen 27104 Wizard SV Gel and PCR Clean-up system Promega A9282 TURBO DNase kit Thermo Fisher AM2238 SuperScript III Reverse Transcriptase Thermo Fisher 1808044 Platinum SYBR Green qPCR SuperMix Thermo Fisher 11733046 Ribolock RNase Inhibitor Thermo Fisher EO0381 RiboCop rRNA Depletion kit Lexogen GmbH 037.96 Protein G Dynabeads Thermo Fisher 10009D Lipofectamine 3000 Transfection Reagent Thermo Fisher L300001 Viafect Transfection Reagent Promega E4981 NEBuilder HiFi DNA Assembly cloning kit NEB E5520S GeneJET PCR Purification Kit Thermo Fisher K0701 (Continued on next page) Molecular Cell 82, 2505–2518.e1–e7, July 7, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data NEXTS overall reconstruction This paper EMDB: 14510 PDB: 7Z4Y NEXTS dimerization module This paper EMDB: 14511 PDB: 7Z4Z NEXTL single protomer This paper EMDB: 14514 NEXTL focused on MTR4 This paper EMDB: 14513 PDB: 7Z52 NEXTS with nuclear exosome This paper EMDB: 14515 Raw and analyzed data This paper Mendeley doi: https://doi.org/10.17632/ m5pg349jth.1 Experimental models: Cell lines HeLa:TIR1 Prof. Edouard Bertrand N/A HeLa:TIR1 ZCCHC8-3F-mAID This study N/A HeLa:TIR1 ZCCHC8-3F-mAID MYCZCCHC81-707 This study N/A HeLa:TIR1 ZCCHC8-3F-mAID MYCZCCHC8177-707 This study N/A Oligonucleotides sgRNA oligonucleotides See Table S2 N/A RT-qPCR oligonucleotides See Table S3 N/A RNA U20 ELLA Biotech N/A RNA CUACCCCGAGAGGGGUAG-U60 ELLA Biotech N/A Recombinant DNA pGCT[hZCCHC8-3F-mAID] HYG This study N/A pGCT[hZCCHC8-3F-mAID] NEO This study N/A pBAC[MYC-hZCCHC8_1-707] BLAST This study N/A pBAC[MYC-hZCCHC8_177-707] BLAST This study N/A pEC-Kan-His-GST-3C-hMTR4(FL) This study N/A pEC-Kan-His-GST-3C-hZCCHC8(41-337) Falk et al. (2016) N/A pEC-Kan-His-GST-3C-hZCCHC8(177-337) This study N/A pEC-Kan-His-GST-3C-hZCCHC8(187-337) This study N/A pEC-Kan-His-GST-3C-hZCCHC8(659707)-TRX This study N/A pEC-Strep-His-Ztag-3C-hRBM7(1-98) Falk et al. (2016) N/A pEC-Kan-His-SUMO-hZCCHC8(D416-506) Adapted from Puno and Lima (2018) N/A pEC-Amp-His-SUMO-hRBM7(1-98) This study N/A Software and algorithms ImageJ (v1.51) Schneider et al. (2012) https://imagej.nih.gov/ij/ AriaMx (v1.71) Agilent https://www.agilent.com/ Graphpad Prism (9.0.0) Graphpad https://www.graphpad.com/scientific- software/prism/ AlphaFold Jumper et al. (2021) https://alphafold.ebi.ac.uk/ AlphaFold_advanced Google Colab notebook Mirdita et al. (2021) https://colab.research.google.com/github/ sokrypton/ColabFold/blob/main/beta/ AlphaFold2_advanced.ipynb SerialEM Schorb et al. (2019) https://bio3d.colorado.edu/SerialEM/ Focus Biyani et al. (2017) https://www.focus-em.org MotionCor2 Zheng et al. (2017) https://msg.ucsf.edu/em/ software/ motioncor2.html (Continued on next page) ll OPEN ACCESS Article e2 Molecular Cell 82, 2505–2518.e1–e7, July 7, 2022

    SYBR Green Assay:

    Article Title: Structure and regulation of the nuclear exosome targeting complex guides RNA substrates to the exosome
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-FLAG M2 Sigma-Aldrich Cat# F1804; RRID: AB_262044 Rabbit polyclonal anti-MTR4 (SKIV2L2) Abcam Cat# ab70551; RRID: AB_1270701 Rabbit monoclonal anti-MYC Cell Signaling Cat# 2278; RRID: AB_490778 Mouse monoclonal anti-MYC Abcam Cat# ab32; RRID:AB_303599 Rabbit polyclonal anti-RBM7 Sigma-Aldrich Cat# HPA013993; RRID:AB_1856137 Rabbit polyclonal anti-ALPHA-TUBULIN Rockland Cat# 600-401-880, RRID:AB_2137000 Bacterial and virus strains BL21 Star (DE3) pRARE E.coli strain EMBL Heidelberg Core Facility N/A Chemicals, peptides, and recombinant proteins H. sapiens MTR4 Lingaraju et al. (2019a); this paper N/A H. sapiens ZCCHC8 Falk et al. (2016), Puno and Lima (2018); this paper N/A H. sapiens RBM7 Falk et al. (2016); this paper N/A H. sapiens EXO10-MPP6-RRP6N-RRP47 Gerlach et al. (2018) N/A T4 DNA polymerase NEB NEB M0203L T1 RNase Thermo Fisher EN0541 Benzonase Merck 71206 3C Prescission protease MPIB core facility N/A Sup2 SUMO protease MPIB core facility N/A ATP, CTP, GTP, UTP Jena Bioscience NU-1010 – 1013 UTP [⍺-32P] Hartmann Analytic FP-210 Indole-3-acetic acid sodium salt (IAA) Sigma-Aldrich I5148-10G Trizol Thermo Fisher 15596026 phenol:chloroform:isoamyl alcohol (25:24:1) Thermo Fisher 15593031 n-octyl-ß-D-glucoside Sigma-Aldrich 850511P AMPPNP Jena Bioscience NU-407-10 BS3 (bis(sulfosuccinimidyl)suberate) Thermo Fisher A39266 Critical commercial assays Phusion Flash High-Fidelity PCR Master Mix Thermo Fisher F548S QIA prep Spin Miniprep Kit Qiagen 27104 Wizard SV Gel and PCR Clean-up system Promega A9282 TURBO DNase kit Thermo Fisher AM2238 SuperScript III Reverse Transcriptase Thermo Fisher 1808044 Platinum SYBR Green qPCR SuperMix Thermo Fisher 11733046 Ribolock RNase Inhibitor Thermo Fisher EO0381 RiboCop rRNA Depletion kit Lexogen GmbH 037.96 Protein G Dynabeads Thermo Fisher 10009D Lipofectamine 3000 Transfection Reagent Thermo Fisher L300001 Viafect Transfection Reagent Promega E4981 NEBuilder HiFi DNA Assembly cloning kit NEB E5520S GeneJET PCR Purification Kit Thermo Fisher K0701 (Continued on next page) Molecular Cell 82, 2505–2518.e1–e7, July 7, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data NEXTS overall reconstruction This paper EMDB: 14510 PDB: 7Z4Y NEXTS dimerization module This paper EMDB: 14511 PDB: 7Z4Z NEXTL single protomer This paper EMDB: 14514 NEXTL focused on MTR4 This paper EMDB: 14513 PDB: 7Z52 NEXTS with nuclear exosome This paper EMDB: 14515 Raw and analyzed data This paper Mendeley doi: https://doi.org/10.17632/ m5pg349jth.1 Experimental models: Cell lines HeLa:TIR1 Prof. Edouard Bertrand N/A HeLa:TIR1 ZCCHC8-3F-mAID This study N/A HeLa:TIR1 ZCCHC8-3F-mAID MYCZCCHC81-707 This study N/A HeLa:TIR1 ZCCHC8-3F-mAID MYCZCCHC8177-707 This study N/A Oligonucleotides sgRNA oligonucleotides See Table S2 N/A RT-qPCR oligonucleotides See Table S3 N/A RNA U20 ELLA Biotech N/A RNA CUACCCCGAGAGGGGUAG-U60 ELLA Biotech N/A Recombinant DNA pGCT[hZCCHC8-3F-mAID] HYG This study N/A pGCT[hZCCHC8-3F-mAID] NEO This study N/A pBAC[MYC-hZCCHC8_1-707] BLAST This study N/A pBAC[MYC-hZCCHC8_177-707] BLAST This study N/A pEC-Kan-His-GST-3C-hMTR4(FL) This study N/A pEC-Kan-His-GST-3C-hZCCHC8(41-337) Falk et al. (2016) N/A pEC-Kan-His-GST-3C-hZCCHC8(177-337) This study N/A pEC-Kan-His-GST-3C-hZCCHC8(187-337) This study N/A pEC-Kan-His-GST-3C-hZCCHC8(659707)-TRX This study N/A pEC-Strep-His-Ztag-3C-hRBM7(1-98) Falk et al. (2016) N/A pEC-Kan-His-SUMO-hZCCHC8(D416-506) Adapted from Puno and Lima (2018) N/A pEC-Amp-His-SUMO-hRBM7(1-98) This study N/A Software and algorithms ImageJ (v1.51) Schneider et al. (2012) https://imagej.nih.gov/ij/ AriaMx (v1.71) Agilent https://www.agilent.com/ Graphpad Prism (9.0.0) Graphpad https://www.graphpad.com/scientific- software/prism/ AlphaFold Jumper et al. (2021) https://alphafold.ebi.ac.uk/ AlphaFold_advanced Google Colab notebook Mirdita et al. (2021) https://colab.research.google.com/github/ sokrypton/ColabFold/blob/main/beta/ AlphaFold2_advanced.ipynb SerialEM Schorb et al. (2019) https://bio3d.colorado.edu/SerialEM/ Focus Biyani et al. (2017) https://www.focus-em.org MotionCor2 Zheng et al. (2017) https://msg.ucsf.edu/em/ software/ motioncor2.html (Continued on next page) ll OPEN ACCESS Article e2 Molecular Cell 82, 2505–2518.e1–e7, July 7, 2022

    Real-time Polymerase Chain Reaction:

    Article Title: Structure and regulation of the nuclear exosome targeting complex guides RNA substrates to the exosome
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-FLAG M2 Sigma-Aldrich Cat# F1804; RRID: AB_262044 Rabbit polyclonal anti-MTR4 (SKIV2L2) Abcam Cat# ab70551; RRID: AB_1270701 Rabbit monoclonal anti-MYC Cell Signaling Cat# 2278; RRID: AB_490778 Mouse monoclonal anti-MYC Abcam Cat# ab32; RRID:AB_303599 Rabbit polyclonal anti-RBM7 Sigma-Aldrich Cat# HPA013993; RRID:AB_1856137 Rabbit polyclonal anti-ALPHA-TUBULIN Rockland Cat# 600-401-880, RRID:AB_2137000 Bacterial and virus strains BL21 Star (DE3) pRARE E.coli strain EMBL Heidelberg Core Facility N/A Chemicals, peptides, and recombinant proteins H. sapiens MTR4 Lingaraju et al. (2019a); this paper N/A H. sapiens ZCCHC8 Falk et al. (2016), Puno and Lima (2018); this paper N/A H. sapiens RBM7 Falk et al. (2016); this paper N/A H. sapiens EXO10-MPP6-RRP6N-RRP47 Gerlach et al. (2018) N/A T4 DNA polymerase NEB NEB M0203L T1 RNase Thermo Fisher EN0541 Benzonase Merck 71206 3C Prescission protease MPIB core facility N/A Sup2 SUMO protease MPIB core facility N/A ATP, CTP, GTP, UTP Jena Bioscience NU-1010 – 1013 UTP [⍺-32P] Hartmann Analytic FP-210 Indole-3-acetic acid sodium salt (IAA) Sigma-Aldrich I5148-10G Trizol Thermo Fisher 15596026 phenol:chloroform:isoamyl alcohol (25:24:1) Thermo Fisher 15593031 n-octyl-ß-D-glucoside Sigma-Aldrich 850511P AMPPNP Jena Bioscience NU-407-10 BS3 (bis(sulfosuccinimidyl)suberate) Thermo Fisher A39266 Critical commercial assays Phusion Flash High-Fidelity PCR Master Mix Thermo Fisher F548S QIA prep Spin Miniprep Kit Qiagen 27104 Wizard SV Gel and PCR Clean-up system Promega A9282 TURBO DNase kit Thermo Fisher AM2238 SuperScript III Reverse Transcriptase Thermo Fisher 1808044 Platinum SYBR Green qPCR SuperMix Thermo Fisher 11733046 Ribolock RNase Inhibitor Thermo Fisher EO0381 RiboCop rRNA Depletion kit Lexogen GmbH 037.96 Protein G Dynabeads Thermo Fisher 10009D Lipofectamine 3000 Transfection Reagent Thermo Fisher L300001 Viafect Transfection Reagent Promega E4981 NEBuilder HiFi DNA Assembly cloning kit NEB E5520S GeneJET PCR Purification Kit Thermo Fisher K0701 (Continued on next page) Molecular Cell 82, 2505–2518.e1–e7, July 7, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data NEXTS overall reconstruction This paper EMDB: 14510 PDB: 7Z4Y NEXTS dimerization module This paper EMDB: 14511 PDB: 7Z4Z NEXTL single protomer This paper EMDB: 14514 NEXTL focused on MTR4 This paper EMDB: 14513 PDB: 7Z52 NEXTS with nuclear exosome This paper EMDB: 14515 Raw and analyzed data This paper Mendeley doi: https://doi.org/10.17632/ m5pg349jth.1 Experimental models: Cell lines HeLa:TIR1 Prof. Edouard Bertrand N/A HeLa:TIR1 ZCCHC8-3F-mAID This study N/A HeLa:TIR1 ZCCHC8-3F-mAID MYCZCCHC81-707 This study N/A HeLa:TIR1 ZCCHC8-3F-mAID MYCZCCHC8177-707 This study N/A Oligonucleotides sgRNA oligonucleotides See Table S2 N/A RT-qPCR oligonucleotides See Table S3 N/A RNA U20 ELLA Biotech N/A RNA CUACCCCGAGAGGGGUAG-U60 ELLA Biotech N/A Recombinant DNA pGCT[hZCCHC8-3F-mAID] HYG This study N/A pGCT[hZCCHC8-3F-mAID] NEO This study N/A pBAC[MYC-hZCCHC8_1-707] BLAST This study N/A pBAC[MYC-hZCCHC8_177-707] BLAST This study N/A pEC-Kan-His-GST-3C-hMTR4(FL) This study N/A pEC-Kan-His-GST-3C-hZCCHC8(41-337) Falk et al. (2016) N/A pEC-Kan-His-GST-3C-hZCCHC8(177-337) This study N/A pEC-Kan-His-GST-3C-hZCCHC8(187-337) This study N/A pEC-Kan-His-GST-3C-hZCCHC8(659707)-TRX This study N/A pEC-Strep-His-Ztag-3C-hRBM7(1-98) Falk et al. (2016) N/A pEC-Kan-His-SUMO-hZCCHC8(D416-506) Adapted from Puno and Lima (2018) N/A pEC-Amp-His-SUMO-hRBM7(1-98) This study N/A Software and algorithms ImageJ (v1.51) Schneider et al. (2012) https://imagej.nih.gov/ij/ AriaMx (v1.71) Agilent https://www.agilent.com/ Graphpad Prism (9.0.0) Graphpad https://www.graphpad.com/scientific- software/prism/ AlphaFold Jumper et al. (2021) https://alphafold.ebi.ac.uk/ AlphaFold_advanced Google Colab notebook Mirdita et al. (2021) https://colab.research.google.com/github/ sokrypton/ColabFold/blob/main/beta/ AlphaFold2_advanced.ipynb SerialEM Schorb et al. (2019) https://bio3d.colorado.edu/SerialEM/ Focus Biyani et al. (2017) https://www.focus-em.org MotionCor2 Zheng et al. (2017) https://msg.ucsf.edu/em/ software/ motioncor2.html (Continued on next page) ll OPEN ACCESS Article e2 Molecular Cell 82, 2505–2518.e1–e7, July 7, 2022

    Transfection:

    Article Title: Structure and regulation of the nuclear exosome targeting complex guides RNA substrates to the exosome
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-FLAG M2 Sigma-Aldrich Cat# F1804; RRID: AB_262044 Rabbit polyclonal anti-MTR4 (SKIV2L2) Abcam Cat# ab70551; RRID: AB_1270701 Rabbit monoclonal anti-MYC Cell Signaling Cat# 2278; RRID: AB_490778 Mouse monoclonal anti-MYC Abcam Cat# ab32; RRID:AB_303599 Rabbit polyclonal anti-RBM7 Sigma-Aldrich Cat# HPA013993; RRID:AB_1856137 Rabbit polyclonal anti-ALPHA-TUBULIN Rockland Cat# 600-401-880, RRID:AB_2137000 Bacterial and virus strains BL21 Star (DE3) pRARE E.coli strain EMBL Heidelberg Core Facility N/A Chemicals, peptides, and recombinant proteins H. sapiens MTR4 Lingaraju et al. (2019a); this paper N/A H. sapiens ZCCHC8 Falk et al. (2016), Puno and Lima (2018); this paper N/A H. sapiens RBM7 Falk et al. (2016); this paper N/A H. sapiens EXO10-MPP6-RRP6N-RRP47 Gerlach et al. (2018) N/A T4 DNA polymerase NEB NEB M0203L T1 RNase Thermo Fisher EN0541 Benzonase Merck 71206 3C Prescission protease MPIB core facility N/A Sup2 SUMO protease MPIB core facility N/A ATP, CTP, GTP, UTP Jena Bioscience NU-1010 – 1013 UTP [⍺-32P] Hartmann Analytic FP-210 Indole-3-acetic acid sodium salt (IAA) Sigma-Aldrich I5148-10G Trizol Thermo Fisher 15596026 phenol:chloroform:isoamyl alcohol (25:24:1) Thermo Fisher 15593031 n-octyl-ß-D-glucoside Sigma-Aldrich 850511P AMPPNP Jena Bioscience NU-407-10 BS3 (bis(sulfosuccinimidyl)suberate) Thermo Fisher A39266 Critical commercial assays Phusion Flash High-Fidelity PCR Master Mix Thermo Fisher F548S QIA prep Spin Miniprep Kit Qiagen 27104 Wizard SV Gel and PCR Clean-up system Promega A9282 TURBO DNase kit Thermo Fisher AM2238 SuperScript III Reverse Transcriptase Thermo Fisher 1808044 Platinum SYBR Green qPCR SuperMix Thermo Fisher 11733046 Ribolock RNase Inhibitor Thermo Fisher EO0381 RiboCop rRNA Depletion kit Lexogen GmbH 037.96 Protein G Dynabeads Thermo Fisher 10009D Lipofectamine 3000 Transfection Reagent Thermo Fisher L300001 Viafect Transfection Reagent Promega E4981 NEBuilder HiFi DNA Assembly cloning kit NEB E5520S GeneJET PCR Purification Kit Thermo Fisher K0701 (Continued on next page) Molecular Cell 82, 2505–2518.e1–e7, July 7, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data NEXTS overall reconstruction This paper EMDB: 14510 PDB: 7Z4Y NEXTS dimerization module This paper EMDB: 14511 PDB: 7Z4Z NEXTL single protomer This paper EMDB: 14514 NEXTL focused on MTR4 This paper EMDB: 14513 PDB: 7Z52 NEXTS with nuclear exosome This paper EMDB: 14515 Raw and analyzed data This paper Mendeley doi: https://doi.org/10.17632/ m5pg349jth.1 Experimental models: Cell lines HeLa:TIR1 Prof. Edouard Bertrand N/A HeLa:TIR1 ZCCHC8-3F-mAID This study N/A HeLa:TIR1 ZCCHC8-3F-mAID MYCZCCHC81-707 This study N/A HeLa:TIR1 ZCCHC8-3F-mAID MYCZCCHC8177-707 This study N/A Oligonucleotides sgRNA oligonucleotides See Table S2 N/A RT-qPCR oligonucleotides See Table S3 N/A RNA U20 ELLA Biotech N/A RNA CUACCCCGAGAGGGGUAG-U60 ELLA Biotech N/A Recombinant DNA pGCT[hZCCHC8-3F-mAID] HYG This study N/A pGCT[hZCCHC8-3F-mAID] NEO This study N/A pBAC[MYC-hZCCHC8_1-707] BLAST This study N/A pBAC[MYC-hZCCHC8_177-707] BLAST This study N/A pEC-Kan-His-GST-3C-hMTR4(FL) This study N/A pEC-Kan-His-GST-3C-hZCCHC8(41-337) Falk et al. (2016) N/A pEC-Kan-His-GST-3C-hZCCHC8(177-337) This study N/A pEC-Kan-His-GST-3C-hZCCHC8(187-337) This study N/A pEC-Kan-His-GST-3C-hZCCHC8(659707)-TRX This study N/A pEC-Strep-His-Ztag-3C-hRBM7(1-98) Falk et al. (2016) N/A pEC-Kan-His-SUMO-hZCCHC8(D416-506) Adapted from Puno and Lima (2018) N/A pEC-Amp-His-SUMO-hRBM7(1-98) This study N/A Software and algorithms ImageJ (v1.51) Schneider et al. (2012) https://imagej.nih.gov/ij/ AriaMx (v1.71) Agilent https://www.agilent.com/ Graphpad Prism (9.0.0) Graphpad https://www.graphpad.com/scientific- software/prism/ AlphaFold Jumper et al. (2021) https://alphafold.ebi.ac.uk/ AlphaFold_advanced Google Colab notebook Mirdita et al. (2021) https://colab.research.google.com/github/ sokrypton/ColabFold/blob/main/beta/ AlphaFold2_advanced.ipynb SerialEM Schorb et al. (2019) https://bio3d.colorado.edu/SerialEM/ Focus Biyani et al. (2017) https://www.focus-em.org MotionCor2 Zheng et al. (2017) https://msg.ucsf.edu/em/ software/ motioncor2.html (Continued on next page) ll OPEN ACCESS Article e2 Molecular Cell 82, 2505–2518.e1–e7, July 7, 2022

    Cloning:

    Article Title: Structure and regulation of the nuclear exosome targeting complex guides RNA substrates to the exosome
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-FLAG M2 Sigma-Aldrich Cat# F1804; RRID: AB_262044 Rabbit polyclonal anti-MTR4 (SKIV2L2) Abcam Cat# ab70551; RRID: AB_1270701 Rabbit monoclonal anti-MYC Cell Signaling Cat# 2278; RRID: AB_490778 Mouse monoclonal anti-MYC Abcam Cat# ab32; RRID:AB_303599 Rabbit polyclonal anti-RBM7 Sigma-Aldrich Cat# HPA013993; RRID:AB_1856137 Rabbit polyclonal anti-ALPHA-TUBULIN Rockland Cat# 600-401-880, RRID:AB_2137000 Bacterial and virus strains BL21 Star (DE3) pRARE E.coli strain EMBL Heidelberg Core Facility N/A Chemicals, peptides, and recombinant proteins H. sapiens MTR4 Lingaraju et al. (2019a); this paper N/A H. sapiens ZCCHC8 Falk et al. (2016), Puno and Lima (2018); this paper N/A H. sapiens RBM7 Falk et al. (2016); this paper N/A H. sapiens EXO10-MPP6-RRP6N-RRP47 Gerlach et al. (2018) N/A T4 DNA polymerase NEB NEB M0203L T1 RNase Thermo Fisher EN0541 Benzonase Merck 71206 3C Prescission protease MPIB core facility N/A Sup2 SUMO protease MPIB core facility N/A ATP, CTP, GTP, UTP Jena Bioscience NU-1010 – 1013 UTP [⍺-32P] Hartmann Analytic FP-210 Indole-3-acetic acid sodium salt (IAA) Sigma-Aldrich I5148-10G Trizol Thermo Fisher 15596026 phenol:chloroform:isoamyl alcohol (25:24:1) Thermo Fisher 15593031 n-octyl-ß-D-glucoside Sigma-Aldrich 850511P AMPPNP Jena Bioscience NU-407-10 BS3 (bis(sulfosuccinimidyl)suberate) Thermo Fisher A39266 Critical commercial assays Phusion Flash High-Fidelity PCR Master Mix Thermo Fisher F548S QIA prep Spin Miniprep Kit Qiagen 27104 Wizard SV Gel and PCR Clean-up system Promega A9282 TURBO DNase kit Thermo Fisher AM2238 SuperScript III Reverse Transcriptase Thermo Fisher 1808044 Platinum SYBR Green qPCR SuperMix Thermo Fisher 11733046 Ribolock RNase Inhibitor Thermo Fisher EO0381 RiboCop rRNA Depletion kit Lexogen GmbH 037.96 Protein G Dynabeads Thermo Fisher 10009D Lipofectamine 3000 Transfection Reagent Thermo Fisher L300001 Viafect Transfection Reagent Promega E4981 NEBuilder HiFi DNA Assembly cloning kit NEB E5520S GeneJET PCR Purification Kit Thermo Fisher K0701 (Continued on next page) Molecular Cell 82, 2505–2518.e1–e7, July 7, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data NEXTS overall reconstruction This paper EMDB: 14510 PDB: 7Z4Y NEXTS dimerization module This paper EMDB: 14511 PDB: 7Z4Z NEXTL single protomer This paper EMDB: 14514 NEXTL focused on MTR4 This paper EMDB: 14513 PDB: 7Z52 NEXTS with nuclear exosome This paper EMDB: 14515 Raw and analyzed data This paper Mendeley doi: https://doi.org/10.17632/ m5pg349jth.1 Experimental models: Cell lines HeLa:TIR1 Prof. Edouard Bertrand N/A HeLa:TIR1 ZCCHC8-3F-mAID This study N/A HeLa:TIR1 ZCCHC8-3F-mAID MYCZCCHC81-707 This study N/A HeLa:TIR1 ZCCHC8-3F-mAID MYCZCCHC8177-707 This study N/A Oligonucleotides sgRNA oligonucleotides See Table S2 N/A RT-qPCR oligonucleotides See Table S3 N/A RNA U20 ELLA Biotech N/A RNA CUACCCCGAGAGGGGUAG-U60 ELLA Biotech N/A Recombinant DNA pGCT[hZCCHC8-3F-mAID] HYG This study N/A pGCT[hZCCHC8-3F-mAID] NEO This study N/A pBAC[MYC-hZCCHC8_1-707] BLAST This study N/A pBAC[MYC-hZCCHC8_177-707] BLAST This study N/A pEC-Kan-His-GST-3C-hMTR4(FL) This study N/A pEC-Kan-His-GST-3C-hZCCHC8(41-337) Falk et al. (2016) N/A pEC-Kan-His-GST-3C-hZCCHC8(177-337) This study N/A pEC-Kan-His-GST-3C-hZCCHC8(187-337) This study N/A pEC-Kan-His-GST-3C-hZCCHC8(659707)-TRX This study N/A pEC-Strep-His-Ztag-3C-hRBM7(1-98) Falk et al. (2016) N/A pEC-Kan-His-SUMO-hZCCHC8(D416-506) Adapted from Puno and Lima (2018) N/A pEC-Amp-His-SUMO-hRBM7(1-98) This study N/A Software and algorithms ImageJ (v1.51) Schneider et al. (2012) https://imagej.nih.gov/ij/ AriaMx (v1.71) Agilent https://www.agilent.com/ Graphpad Prism (9.0.0) Graphpad https://www.graphpad.com/scientific- software/prism/ AlphaFold Jumper et al. (2021) https://alphafold.ebi.ac.uk/ AlphaFold_advanced Google Colab notebook Mirdita et al. (2021) https://colab.research.google.com/github/ sokrypton/ColabFold/blob/main/beta/ AlphaFold2_advanced.ipynb SerialEM Schorb et al. (2019) https://bio3d.colorado.edu/SerialEM/ Focus Biyani et al. (2017) https://www.focus-em.org MotionCor2 Zheng et al. (2017) https://msg.ucsf.edu/em/ software/ motioncor2.html (Continued on next page) ll OPEN ACCESS Article e2 Molecular Cell 82, 2505–2518.e1–e7, July 7, 2022

    Purification:

    Article Title: Structure and regulation of the nuclear exosome targeting complex guides RNA substrates to the exosome
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-FLAG M2 Sigma-Aldrich Cat# F1804; RRID: AB_262044 Rabbit polyclonal anti-MTR4 (SKIV2L2) Abcam Cat# ab70551; RRID: AB_1270701 Rabbit monoclonal anti-MYC Cell Signaling Cat# 2278; RRID: AB_490778 Mouse monoclonal anti-MYC Abcam Cat# ab32; RRID:AB_303599 Rabbit polyclonal anti-RBM7 Sigma-Aldrich Cat# HPA013993; RRID:AB_1856137 Rabbit polyclonal anti-ALPHA-TUBULIN Rockland Cat# 600-401-880, RRID:AB_2137000 Bacterial and virus strains BL21 Star (DE3) pRARE E.coli strain EMBL Heidelberg Core Facility N/A Chemicals, peptides, and recombinant proteins H. sapiens MTR4 Lingaraju et al. (2019a); this paper N/A H. sapiens ZCCHC8 Falk et al. (2016), Puno and Lima (2018); this paper N/A H. sapiens RBM7 Falk et al. (2016); this paper N/A H. sapiens EXO10-MPP6-RRP6N-RRP47 Gerlach et al. (2018) N/A T4 DNA polymerase NEB NEB M0203L T1 RNase Thermo Fisher EN0541 Benzonase Merck 71206 3C Prescission protease MPIB core facility N/A Sup2 SUMO protease MPIB core facility N/A ATP, CTP, GTP, UTP Jena Bioscience NU-1010 – 1013 UTP [⍺-32P] Hartmann Analytic FP-210 Indole-3-acetic acid sodium salt (IAA) Sigma-Aldrich I5148-10G Trizol Thermo Fisher 15596026 phenol:chloroform:isoamyl alcohol (25:24:1) Thermo Fisher 15593031 n-octyl-ß-D-glucoside Sigma-Aldrich 850511P AMPPNP Jena Bioscience NU-407-10 BS3 (bis(sulfosuccinimidyl)suberate) Thermo Fisher A39266 Critical commercial assays Phusion Flash High-Fidelity PCR Master Mix Thermo Fisher F548S QIA prep Spin Miniprep Kit Qiagen 27104 Wizard SV Gel and PCR Clean-up system Promega A9282 TURBO DNase kit Thermo Fisher AM2238 SuperScript III Reverse Transcriptase Thermo Fisher 1808044 Platinum SYBR Green qPCR SuperMix Thermo Fisher 11733046 Ribolock RNase Inhibitor Thermo Fisher EO0381 RiboCop rRNA Depletion kit Lexogen GmbH 037.96 Protein G Dynabeads Thermo Fisher 10009D Lipofectamine 3000 Transfection Reagent Thermo Fisher L300001 Viafect Transfection Reagent Promega E4981 NEBuilder HiFi DNA Assembly cloning kit NEB E5520S GeneJET PCR Purification Kit Thermo Fisher K0701 (Continued on next page) Molecular Cell 82, 2505–2518.e1–e7, July 7, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data NEXTS overall reconstruction This paper EMDB: 14510 PDB: 7Z4Y NEXTS dimerization module This paper EMDB: 14511 PDB: 7Z4Z NEXTL single protomer This paper EMDB: 14514 NEXTL focused on MTR4 This paper EMDB: 14513 PDB: 7Z52 NEXTS with nuclear exosome This paper EMDB: 14515 Raw and analyzed data This paper Mendeley doi: https://doi.org/10.17632/ m5pg349jth.1 Experimental models: Cell lines HeLa:TIR1 Prof. Edouard Bertrand N/A HeLa:TIR1 ZCCHC8-3F-mAID This study N/A HeLa:TIR1 ZCCHC8-3F-mAID MYCZCCHC81-707 This study N/A HeLa:TIR1 ZCCHC8-3F-mAID MYCZCCHC8177-707 This study N/A Oligonucleotides sgRNA oligonucleotides See Table S2 N/A RT-qPCR oligonucleotides See Table S3 N/A RNA U20 ELLA Biotech N/A RNA CUACCCCGAGAGGGGUAG-U60 ELLA Biotech N/A Recombinant DNA pGCT[hZCCHC8-3F-mAID] HYG This study N/A pGCT[hZCCHC8-3F-mAID] NEO This study N/A pBAC[MYC-hZCCHC8_1-707] BLAST This study N/A pBAC[MYC-hZCCHC8_177-707] BLAST This study N/A pEC-Kan-His-GST-3C-hMTR4(FL) This study N/A pEC-Kan-His-GST-3C-hZCCHC8(41-337) Falk et al. (2016) N/A pEC-Kan-His-GST-3C-hZCCHC8(177-337) This study N/A pEC-Kan-His-GST-3C-hZCCHC8(187-337) This study N/A pEC-Kan-His-GST-3C-hZCCHC8(659707)-TRX This study N/A pEC-Strep-His-Ztag-3C-hRBM7(1-98) Falk et al. (2016) N/A pEC-Kan-His-SUMO-hZCCHC8(D416-506) Adapted from Puno and Lima (2018) N/A pEC-Amp-His-SUMO-hRBM7(1-98) This study N/A Software and algorithms ImageJ (v1.51) Schneider et al. (2012) https://imagej.nih.gov/ij/ AriaMx (v1.71) Agilent https://www.agilent.com/ Graphpad Prism (9.0.0) Graphpad https://www.graphpad.com/scientific- software/prism/ AlphaFold Jumper et al. (2021) https://alphafold.ebi.ac.uk/ AlphaFold_advanced Google Colab notebook Mirdita et al. (2021) https://colab.research.google.com/github/ sokrypton/ColabFold/blob/main/beta/ AlphaFold2_advanced.ipynb SerialEM Schorb et al. (2019) https://bio3d.colorado.edu/SerialEM/ Focus Biyani et al. (2017) https://www.focus-em.org MotionCor2 Zheng et al. (2017) https://msg.ucsf.edu/em/ software/ motioncor2.html (Continued on next page) ll OPEN ACCESS Article e2 Molecular Cell 82, 2505–2518.e1–e7, July 7, 2022



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