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paper emdb emd 44335 adar1 variants rna seq  (ATCC)


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    ATCC paper emdb emd 44335 adar1 variants rna seq
    Paper Emdb Emd 44335 Adar1 Variants Rna Seq, supplied by ATCC, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/paper+emdb+emd+44335+adar1+variants+rna+seq/Arthroderma+otae+(Hasegawa+et+Usui)+McGinnis+et+al/pm40101712-209-67-89
    Average 94 stars, based on 1 article reviews
    paper emdb emd 44335 adar1 variants rna seq - by Bioz Stars, 2026-10
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    RNA sequencing:

    Article Title: Biochemical profiling and structural basis of ADAR1-mediated RNA editing.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins AgeI NEB Cat#R3552 XbaI NEB Cat#R0145S HindIII NEB Cat#R3104 Antarctic Phosphatase NEB Cat#M0289S T4 polynucleotide kinase NEB Cat#M0201S Amylose resin NEB Cat#E8021L IPTG Sigma-Aldrich Cat#I6758 2-Mercaptoethanol Sigma-Aldrich Cat#M3148 Phenylmethylsulfonyl fluoride Sigma-Aldrich Cat#11359061001 Spermidine Sigma-Aldrich Cat#85558 sodium butyrate Sigma-Aldrich Cat#303410-100 KCl Sigma-Aldrich Cat#P9541-1KG HEPES Sigma-Aldrich Cat#H3375-500G DTT Sigma-Aldrich Cat#11583786001 ZnCl2 Sigma-Aldrich Cat#1088160250 Glycerol Sigma-Aldrich Cat#G5516-4L PMSF Sigma-Aldrich Cat#P7626-25G Urea Sigma Aldrich Cat#U5128-5KG Maltose Sigma-Aldrich M5885-500G Tris base Sigma-Aldrich Cat#93362-250G NaCl Sigma-Aldrich Cat#S3014-500G 2-Mercaptoethanol Sigma-Aldrich Cat#M3148 Imidazole Sigma-Aldrich Cat#I2399-100G NTP set ThermoFisher Scientific Cat#R0481 Fetal bovine serum ThermoFisher Scientific Cat#16000044 Freestyle medium ThermoFisher Scientific Cat#12338026 Hybridoma medium ThermoFisher Scientific Cat#12045084 Protease inhibitor cocktail ThermoFisher Scientific Cat#A-32965 DEME ATCC Cat#30-2002 L-Glutamine ATCC Cat#30-2214 ATP [g-32P] PerkinElmer Cat#BLU002Z250UC Terrific Broth Novagen Cat#71754-4 Bradford Bradford Kit Cat#B6916-500 Polyethyleneimine Polysciences Cat#23966-1 Nickel-NTA resin Qiagen Cat#30210 Proteins: Wild type ADAR1 and mutants This paper N/A T7 RNA polymerase homemade N/A SEPN2 homemade N/A Prescission protease homemade N/A Tn5 transposase64 homemade N/A SMARTScribe reverse transcriptase Takara Cat#639537 Q5 High-Fidelity 2X Master Mix NEB Cat#M0492L Thermostable RNase H NEB Cat#M0523S (Continued on next page) Molecular Cell 85, 1381–1394.e1–e6, April 3, 2025 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER DNase I (RNase-free) NEB Cat#M0303L Lipofectamine 3000 ThermoFisher Scientific Cat#L3000015 HiScript III RT SuperMix Vazyme Cat#R323-01 Deposited data ADAR1-GLI complex coordinates This paper PDB: 9B83 ADAR1-HT complex coordinates This paper PDB: 9B84 ADAR1-HT complex 2 coordinates This paper PDB: 9B89 ADAR1-GLI complex EM map This paper EMDB: EMD-44331 ADAR1-HT complex EM map This paper EMDB: EMD-44332 ADAR1-HT complex 2 EM map This paper EMDB: EMD-44335 ADAR1 variants RNA-Seq This paper GEO: GSE285023 Original data files This paper https://doi.org/10.17632/r8zwszrjxj.1 Experimental models: Cell lines HEK293T cells ATCC ATTC# CRL-3216 Experimental models: Organisms/strains E. coli Stellar Competent Cells Takara Cat#636767 E. coli Rosetta 2(DE3) Competent Cells Novagen Cat#70954-4 Oligonucleotides DNA primers for cloning This paper Table S1 DNA oligos for IVT template This paper Table S2 RNAs This paper Table S3 rRNA depletion oligos Adiconis et al.65 N/A Recombinant DNA pmGFP-ADAR1-p150 Addgene Addgene plasmid #117927 Wild type pLEXm-ADAR1 and mutants This paper N/A pET-SUMO-EcEndoV This paper N/A pUC19 vector ThermoFisher Scientific Cat#SD0061 Software and algorithms AlphaFold2 in Google CoLab DeepMind and Google https://colab.research.google.com/ github/sokrypton/ColabFold/blob/ main/AlphaFold2.ipynb Relion version 4.0 Kimanius et al.66 https://www3.mrc-lmb.cam.ac.uk/ relion//index.php/Main_Page/; RRID:SCR_016274 MotionCorr2 Zheng et al.67 https://emcore.ucsf.edu/ucsf-software GCTF Zhang68 https://sbgrid.org/software/titles/gctf SerialEM Mastronarde et al.69 https://bio3d.colorado.edu/SerialEM/ Prism (GraphPad) Version 9.4.1 N/A www.graphpad.com cryoSPARC version 3.3 Punjani et al.70 https://cryosparc.com/; RRID:SCR_016501 UCSF Chimera Pettersen et al.71 https://www.cgl.ucsf.edu/chimera/; RRID:SCR_004097 PyMOL N/A https://www.pymol.org/pymol.html Phenix version 1.18.2 Afonine et al.72 https://www.phenix-online.org/; RRID:SCR_014224 Coot version 0.9.6 Emsley and Cowtan73 https://www2.mrc-lmb.cam.ac.uk/ personal/ pemsley/coot/; RRID:SCR_014222 pileup2var Xiao et al.74 https://github.com/shunliubio/pileup2var Other Quantifoil R 1.2/1.3 Cu grids EMS Cat#Q3100CR1.3 Au-Flat 1.2/1.3 AU grids EMS Cat#AUFT313-50 UltrAuFoil R 1.2/1.3 Au grids EMS Cat#Q350AR13A e2 Molecular Cell 85, 1381–1394.e1–e6, April 3, 2025 .. The HEK293T cell was established as an adherent cell line with the culture medium containing DMEM (ATCC, catalog 30-2002), 10% FBS (Thermo Fisher, catalog 16000044), and 1X L-Glutamine (ATCC, catalog 30-2214) in an incubator set at 37 C and 5% CO2, and the cells were then adapted to the suspension growth with suspension culture containing Freestyle medium (Thermo Fisher, catalog 12338026) and 1%FBSwhen the cells reached about 50% confluency.

    Cloning:

    Article Title: Biochemical profiling and structural basis of ADAR1-mediated RNA editing.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins AgeI NEB Cat#R3552 XbaI NEB Cat#R0145S HindIII NEB Cat#R3104 Antarctic Phosphatase NEB Cat#M0289S T4 polynucleotide kinase NEB Cat#M0201S Amylose resin NEB Cat#E8021L IPTG Sigma-Aldrich Cat#I6758 2-Mercaptoethanol Sigma-Aldrich Cat#M3148 Phenylmethylsulfonyl fluoride Sigma-Aldrich Cat#11359061001 Spermidine Sigma-Aldrich Cat#85558 sodium butyrate Sigma-Aldrich Cat#303410-100 KCl Sigma-Aldrich Cat#P9541-1KG HEPES Sigma-Aldrich Cat#H3375-500G DTT Sigma-Aldrich Cat#11583786001 ZnCl2 Sigma-Aldrich Cat#1088160250 Glycerol Sigma-Aldrich Cat#G5516-4L PMSF Sigma-Aldrich Cat#P7626-25G Urea Sigma Aldrich Cat#U5128-5KG Maltose Sigma-Aldrich M5885-500G Tris base Sigma-Aldrich Cat#93362-250G NaCl Sigma-Aldrich Cat#S3014-500G 2-Mercaptoethanol Sigma-Aldrich Cat#M3148 Imidazole Sigma-Aldrich Cat#I2399-100G NTP set ThermoFisher Scientific Cat#R0481 Fetal bovine serum ThermoFisher Scientific Cat#16000044 Freestyle medium ThermoFisher Scientific Cat#12338026 Hybridoma medium ThermoFisher Scientific Cat#12045084 Protease inhibitor cocktail ThermoFisher Scientific Cat#A-32965 DEME ATCC Cat#30-2002 L-Glutamine ATCC Cat#30-2214 ATP [g-32P] PerkinElmer Cat#BLU002Z250UC Terrific Broth Novagen Cat#71754-4 Bradford Bradford Kit Cat#B6916-500 Polyethyleneimine Polysciences Cat#23966-1 Nickel-NTA resin Qiagen Cat#30210 Proteins: Wild type ADAR1 and mutants This paper N/A T7 RNA polymerase homemade N/A SEPN2 homemade N/A Prescission protease homemade N/A Tn5 transposase64 homemade N/A SMARTScribe reverse transcriptase Takara Cat#639537 Q5 High-Fidelity 2X Master Mix NEB Cat#M0492L Thermostable RNase H NEB Cat#M0523S (Continued on next page) Molecular Cell 85, 1381–1394.e1–e6, April 3, 2025 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER DNase I (RNase-free) NEB Cat#M0303L Lipofectamine 3000 ThermoFisher Scientific Cat#L3000015 HiScript III RT SuperMix Vazyme Cat#R323-01 Deposited data ADAR1-GLI complex coordinates This paper PDB: 9B83 ADAR1-HT complex coordinates This paper PDB: 9B84 ADAR1-HT complex 2 coordinates This paper PDB: 9B89 ADAR1-GLI complex EM map This paper EMDB: EMD-44331 ADAR1-HT complex EM map This paper EMDB: EMD-44332 ADAR1-HT complex 2 EM map This paper EMDB: EMD-44335 ADAR1 variants RNA-Seq This paper GEO: GSE285023 Original data files This paper https://doi.org/10.17632/r8zwszrjxj.1 Experimental models: Cell lines HEK293T cells ATCC ATTC# CRL-3216 Experimental models: Organisms/strains E. coli Stellar Competent Cells Takara Cat#636767 E. coli Rosetta 2(DE3) Competent Cells Novagen Cat#70954-4 Oligonucleotides DNA primers for cloning This paper Table S1 DNA oligos for IVT template This paper Table S2 RNAs This paper Table S3 rRNA depletion oligos Adiconis et al.65 N/A Recombinant DNA pmGFP-ADAR1-p150 Addgene Addgene plasmid #117927 Wild type pLEXm-ADAR1 and mutants This paper N/A pET-SUMO-EcEndoV This paper N/A pUC19 vector ThermoFisher Scientific Cat#SD0061 Software and algorithms AlphaFold2 in Google CoLab DeepMind and Google https://colab.research.google.com/ github/sokrypton/ColabFold/blob/ main/AlphaFold2.ipynb Relion version 4.0 Kimanius et al.66 https://www3.mrc-lmb.cam.ac.uk/ relion//index.php/Main_Page/; RRID:SCR_016274 MotionCorr2 Zheng et al.67 https://emcore.ucsf.edu/ucsf-software GCTF Zhang68 https://sbgrid.org/software/titles/gctf SerialEM Mastronarde et al.69 https://bio3d.colorado.edu/SerialEM/ Prism (GraphPad) Version 9.4.1 N/A www.graphpad.com cryoSPARC version 3.3 Punjani et al.70 https://cryosparc.com/; RRID:SCR_016501 UCSF Chimera Pettersen et al.71 https://www.cgl.ucsf.edu/chimera/; RRID:SCR_004097 PyMOL N/A https://www.pymol.org/pymol.html Phenix version 1.18.2 Afonine et al.72 https://www.phenix-online.org/; RRID:SCR_014224 Coot version 0.9.6 Emsley and Cowtan73 https://www2.mrc-lmb.cam.ac.uk/ personal/ pemsley/coot/; RRID:SCR_014222 pileup2var Xiao et al.74 https://github.com/shunliubio/pileup2var Other Quantifoil R 1.2/1.3 Cu grids EMS Cat#Q3100CR1.3 Au-Flat 1.2/1.3 AU grids EMS Cat#AUFT313-50 UltrAuFoil R 1.2/1.3 Au grids EMS Cat#Q350AR13A e2 Molecular Cell 85, 1381–1394.e1–e6, April 3, 2025 .. The HEK293T cell was established as an adherent cell line with the culture medium containing DMEM (ATCC, catalog 30-2002), 10% FBS (Thermo Fisher, catalog 16000044), and 1X L-Glutamine (ATCC, catalog 30-2214) in an incubator set at 37 C and 5% CO2, and the cells were then adapted to the suspension growth with suspension culture containing Freestyle medium (Thermo Fisher, catalog 12338026) and 1%FBSwhen the cells reached about 50% confluency.

    Recombinant:

    Article Title: Biochemical profiling and structural basis of ADAR1-mediated RNA editing.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins AgeI NEB Cat#R3552 XbaI NEB Cat#R0145S HindIII NEB Cat#R3104 Antarctic Phosphatase NEB Cat#M0289S T4 polynucleotide kinase NEB Cat#M0201S Amylose resin NEB Cat#E8021L IPTG Sigma-Aldrich Cat#I6758 2-Mercaptoethanol Sigma-Aldrich Cat#M3148 Phenylmethylsulfonyl fluoride Sigma-Aldrich Cat#11359061001 Spermidine Sigma-Aldrich Cat#85558 sodium butyrate Sigma-Aldrich Cat#303410-100 KCl Sigma-Aldrich Cat#P9541-1KG HEPES Sigma-Aldrich Cat#H3375-500G DTT Sigma-Aldrich Cat#11583786001 ZnCl2 Sigma-Aldrich Cat#1088160250 Glycerol Sigma-Aldrich Cat#G5516-4L PMSF Sigma-Aldrich Cat#P7626-25G Urea Sigma Aldrich Cat#U5128-5KG Maltose Sigma-Aldrich M5885-500G Tris base Sigma-Aldrich Cat#93362-250G NaCl Sigma-Aldrich Cat#S3014-500G 2-Mercaptoethanol Sigma-Aldrich Cat#M3148 Imidazole Sigma-Aldrich Cat#I2399-100G NTP set ThermoFisher Scientific Cat#R0481 Fetal bovine serum ThermoFisher Scientific Cat#16000044 Freestyle medium ThermoFisher Scientific Cat#12338026 Hybridoma medium ThermoFisher Scientific Cat#12045084 Protease inhibitor cocktail ThermoFisher Scientific Cat#A-32965 DEME ATCC Cat#30-2002 L-Glutamine ATCC Cat#30-2214 ATP [g-32P] PerkinElmer Cat#BLU002Z250UC Terrific Broth Novagen Cat#71754-4 Bradford Bradford Kit Cat#B6916-500 Polyethyleneimine Polysciences Cat#23966-1 Nickel-NTA resin Qiagen Cat#30210 Proteins: Wild type ADAR1 and mutants This paper N/A T7 RNA polymerase homemade N/A SEPN2 homemade N/A Prescission protease homemade N/A Tn5 transposase64 homemade N/A SMARTScribe reverse transcriptase Takara Cat#639537 Q5 High-Fidelity 2X Master Mix NEB Cat#M0492L Thermostable RNase H NEB Cat#M0523S (Continued on next page) Molecular Cell 85, 1381–1394.e1–e6, April 3, 2025 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER DNase I (RNase-free) NEB Cat#M0303L Lipofectamine 3000 ThermoFisher Scientific Cat#L3000015 HiScript III RT SuperMix Vazyme Cat#R323-01 Deposited data ADAR1-GLI complex coordinates This paper PDB: 9B83 ADAR1-HT complex coordinates This paper PDB: 9B84 ADAR1-HT complex 2 coordinates This paper PDB: 9B89 ADAR1-GLI complex EM map This paper EMDB: EMD-44331 ADAR1-HT complex EM map This paper EMDB: EMD-44332 ADAR1-HT complex 2 EM map This paper EMDB: EMD-44335 ADAR1 variants RNA-Seq This paper GEO: GSE285023 Original data files This paper https://doi.org/10.17632/r8zwszrjxj.1 Experimental models: Cell lines HEK293T cells ATCC ATTC# CRL-3216 Experimental models: Organisms/strains E. coli Stellar Competent Cells Takara Cat#636767 E. coli Rosetta 2(DE3) Competent Cells Novagen Cat#70954-4 Oligonucleotides DNA primers for cloning This paper Table S1 DNA oligos for IVT template This paper Table S2 RNAs This paper Table S3 rRNA depletion oligos Adiconis et al.65 N/A Recombinant DNA pmGFP-ADAR1-p150 Addgene Addgene plasmid #117927 Wild type pLEXm-ADAR1 and mutants This paper N/A pET-SUMO-EcEndoV This paper N/A pUC19 vector ThermoFisher Scientific Cat#SD0061 Software and algorithms AlphaFold2 in Google CoLab DeepMind and Google https://colab.research.google.com/ github/sokrypton/ColabFold/blob/ main/AlphaFold2.ipynb Relion version 4.0 Kimanius et al.66 https://www3.mrc-lmb.cam.ac.uk/ relion//index.php/Main_Page/; RRID:SCR_016274 MotionCorr2 Zheng et al.67 https://emcore.ucsf.edu/ucsf-software GCTF Zhang68 https://sbgrid.org/software/titles/gctf SerialEM Mastronarde et al.69 https://bio3d.colorado.edu/SerialEM/ Prism (GraphPad) Version 9.4.1 N/A www.graphpad.com cryoSPARC version 3.3 Punjani et al.70 https://cryosparc.com/; RRID:SCR_016501 UCSF Chimera Pettersen et al.71 https://www.cgl.ucsf.edu/chimera/; RRID:SCR_004097 PyMOL N/A https://www.pymol.org/pymol.html Phenix version 1.18.2 Afonine et al.72 https://www.phenix-online.org/; RRID:SCR_014224 Coot version 0.9.6 Emsley and Cowtan73 https://www2.mrc-lmb.cam.ac.uk/ personal/ pemsley/coot/; RRID:SCR_014222 pileup2var Xiao et al.74 https://github.com/shunliubio/pileup2var Other Quantifoil R 1.2/1.3 Cu grids EMS Cat#Q3100CR1.3 Au-Flat 1.2/1.3 AU grids EMS Cat#AUFT313-50 UltrAuFoil R 1.2/1.3 Au grids EMS Cat#Q350AR13A e2 Molecular Cell 85, 1381–1394.e1–e6, April 3, 2025 .. The HEK293T cell was established as an adherent cell line with the culture medium containing DMEM (ATCC, catalog 30-2002), 10% FBS (Thermo Fisher, catalog 16000044), and 1X L-Glutamine (ATCC, catalog 30-2214) in an incubator set at 37 C and 5% CO2, and the cells were then adapted to the suspension growth with suspension culture containing Freestyle medium (Thermo Fisher, catalog 12338026) and 1%FBSwhen the cells reached about 50% confluency.

    Plasmid Preparation:

    Article Title: Biochemical profiling and structural basis of ADAR1-mediated RNA editing.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins AgeI NEB Cat#R3552 XbaI NEB Cat#R0145S HindIII NEB Cat#R3104 Antarctic Phosphatase NEB Cat#M0289S T4 polynucleotide kinase NEB Cat#M0201S Amylose resin NEB Cat#E8021L IPTG Sigma-Aldrich Cat#I6758 2-Mercaptoethanol Sigma-Aldrich Cat#M3148 Phenylmethylsulfonyl fluoride Sigma-Aldrich Cat#11359061001 Spermidine Sigma-Aldrich Cat#85558 sodium butyrate Sigma-Aldrich Cat#303410-100 KCl Sigma-Aldrich Cat#P9541-1KG HEPES Sigma-Aldrich Cat#H3375-500G DTT Sigma-Aldrich Cat#11583786001 ZnCl2 Sigma-Aldrich Cat#1088160250 Glycerol Sigma-Aldrich Cat#G5516-4L PMSF Sigma-Aldrich Cat#P7626-25G Urea Sigma Aldrich Cat#U5128-5KG Maltose Sigma-Aldrich M5885-500G Tris base Sigma-Aldrich Cat#93362-250G NaCl Sigma-Aldrich Cat#S3014-500G 2-Mercaptoethanol Sigma-Aldrich Cat#M3148 Imidazole Sigma-Aldrich Cat#I2399-100G NTP set ThermoFisher Scientific Cat#R0481 Fetal bovine serum ThermoFisher Scientific Cat#16000044 Freestyle medium ThermoFisher Scientific Cat#12338026 Hybridoma medium ThermoFisher Scientific Cat#12045084 Protease inhibitor cocktail ThermoFisher Scientific Cat#A-32965 DEME ATCC Cat#30-2002 L-Glutamine ATCC Cat#30-2214 ATP [g-32P] PerkinElmer Cat#BLU002Z250UC Terrific Broth Novagen Cat#71754-4 Bradford Bradford Kit Cat#B6916-500 Polyethyleneimine Polysciences Cat#23966-1 Nickel-NTA resin Qiagen Cat#30210 Proteins: Wild type ADAR1 and mutants This paper N/A T7 RNA polymerase homemade N/A SEPN2 homemade N/A Prescission protease homemade N/A Tn5 transposase64 homemade N/A SMARTScribe reverse transcriptase Takara Cat#639537 Q5 High-Fidelity 2X Master Mix NEB Cat#M0492L Thermostable RNase H NEB Cat#M0523S (Continued on next page) Molecular Cell 85, 1381–1394.e1–e6, April 3, 2025 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER DNase I (RNase-free) NEB Cat#M0303L Lipofectamine 3000 ThermoFisher Scientific Cat#L3000015 HiScript III RT SuperMix Vazyme Cat#R323-01 Deposited data ADAR1-GLI complex coordinates This paper PDB: 9B83 ADAR1-HT complex coordinates This paper PDB: 9B84 ADAR1-HT complex 2 coordinates This paper PDB: 9B89 ADAR1-GLI complex EM map This paper EMDB: EMD-44331 ADAR1-HT complex EM map This paper EMDB: EMD-44332 ADAR1-HT complex 2 EM map This paper EMDB: EMD-44335 ADAR1 variants RNA-Seq This paper GEO: GSE285023 Original data files This paper https://doi.org/10.17632/r8zwszrjxj.1 Experimental models: Cell lines HEK293T cells ATCC ATTC# CRL-3216 Experimental models: Organisms/strains E. coli Stellar Competent Cells Takara Cat#636767 E. coli Rosetta 2(DE3) Competent Cells Novagen Cat#70954-4 Oligonucleotides DNA primers for cloning This paper Table S1 DNA oligos for IVT template This paper Table S2 RNAs This paper Table S3 rRNA depletion oligos Adiconis et al.65 N/A Recombinant DNA pmGFP-ADAR1-p150 Addgene Addgene plasmid #117927 Wild type pLEXm-ADAR1 and mutants This paper N/A pET-SUMO-EcEndoV This paper N/A pUC19 vector ThermoFisher Scientific Cat#SD0061 Software and algorithms AlphaFold2 in Google CoLab DeepMind and Google https://colab.research.google.com/ github/sokrypton/ColabFold/blob/ main/AlphaFold2.ipynb Relion version 4.0 Kimanius et al.66 https://www3.mrc-lmb.cam.ac.uk/ relion//index.php/Main_Page/; RRID:SCR_016274 MotionCorr2 Zheng et al.67 https://emcore.ucsf.edu/ucsf-software GCTF Zhang68 https://sbgrid.org/software/titles/gctf SerialEM Mastronarde et al.69 https://bio3d.colorado.edu/SerialEM/ Prism (GraphPad) Version 9.4.1 N/A www.graphpad.com cryoSPARC version 3.3 Punjani et al.70 https://cryosparc.com/; RRID:SCR_016501 UCSF Chimera Pettersen et al.71 https://www.cgl.ucsf.edu/chimera/; RRID:SCR_004097 PyMOL N/A https://www.pymol.org/pymol.html Phenix version 1.18.2 Afonine et al.72 https://www.phenix-online.org/; RRID:SCR_014224 Coot version 0.9.6 Emsley and Cowtan73 https://www2.mrc-lmb.cam.ac.uk/ personal/ pemsley/coot/; RRID:SCR_014222 pileup2var Xiao et al.74 https://github.com/shunliubio/pileup2var Other Quantifoil R 1.2/1.3 Cu grids EMS Cat#Q3100CR1.3 Au-Flat 1.2/1.3 AU grids EMS Cat#AUFT313-50 UltrAuFoil R 1.2/1.3 Au grids EMS Cat#Q350AR13A e2 Molecular Cell 85, 1381–1394.e1–e6, April 3, 2025 .. The HEK293T cell was established as an adherent cell line with the culture medium containing DMEM (ATCC, catalog 30-2002), 10% FBS (Thermo Fisher, catalog 16000044), and 1X L-Glutamine (ATCC, catalog 30-2214) in an incubator set at 37 C and 5% CO2, and the cells were then adapted to the suspension growth with suspension culture containing Freestyle medium (Thermo Fisher, catalog 12338026) and 1%FBSwhen the cells reached about 50% confluency.

    Software:

    Article Title: Biochemical profiling and structural basis of ADAR1-mediated RNA editing.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins AgeI NEB Cat#R3552 XbaI NEB Cat#R0145S HindIII NEB Cat#R3104 Antarctic Phosphatase NEB Cat#M0289S T4 polynucleotide kinase NEB Cat#M0201S Amylose resin NEB Cat#E8021L IPTG Sigma-Aldrich Cat#I6758 2-Mercaptoethanol Sigma-Aldrich Cat#M3148 Phenylmethylsulfonyl fluoride Sigma-Aldrich Cat#11359061001 Spermidine Sigma-Aldrich Cat#85558 sodium butyrate Sigma-Aldrich Cat#303410-100 KCl Sigma-Aldrich Cat#P9541-1KG HEPES Sigma-Aldrich Cat#H3375-500G DTT Sigma-Aldrich Cat#11583786001 ZnCl2 Sigma-Aldrich Cat#1088160250 Glycerol Sigma-Aldrich Cat#G5516-4L PMSF Sigma-Aldrich Cat#P7626-25G Urea Sigma Aldrich Cat#U5128-5KG Maltose Sigma-Aldrich M5885-500G Tris base Sigma-Aldrich Cat#93362-250G NaCl Sigma-Aldrich Cat#S3014-500G 2-Mercaptoethanol Sigma-Aldrich Cat#M3148 Imidazole Sigma-Aldrich Cat#I2399-100G NTP set ThermoFisher Scientific Cat#R0481 Fetal bovine serum ThermoFisher Scientific Cat#16000044 Freestyle medium ThermoFisher Scientific Cat#12338026 Hybridoma medium ThermoFisher Scientific Cat#12045084 Protease inhibitor cocktail ThermoFisher Scientific Cat#A-32965 DEME ATCC Cat#30-2002 L-Glutamine ATCC Cat#30-2214 ATP [g-32P] PerkinElmer Cat#BLU002Z250UC Terrific Broth Novagen Cat#71754-4 Bradford Bradford Kit Cat#B6916-500 Polyethyleneimine Polysciences Cat#23966-1 Nickel-NTA resin Qiagen Cat#30210 Proteins: Wild type ADAR1 and mutants This paper N/A T7 RNA polymerase homemade N/A SEPN2 homemade N/A Prescission protease homemade N/A Tn5 transposase64 homemade N/A SMARTScribe reverse transcriptase Takara Cat#639537 Q5 High-Fidelity 2X Master Mix NEB Cat#M0492L Thermostable RNase H NEB Cat#M0523S (Continued on next page) Molecular Cell 85, 1381–1394.e1–e6, April 3, 2025 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER DNase I (RNase-free) NEB Cat#M0303L Lipofectamine 3000 ThermoFisher Scientific Cat#L3000015 HiScript III RT SuperMix Vazyme Cat#R323-01 Deposited data ADAR1-GLI complex coordinates This paper PDB: 9B83 ADAR1-HT complex coordinates This paper PDB: 9B84 ADAR1-HT complex 2 coordinates This paper PDB: 9B89 ADAR1-GLI complex EM map This paper EMDB: EMD-44331 ADAR1-HT complex EM map This paper EMDB: EMD-44332 ADAR1-HT complex 2 EM map This paper EMDB: EMD-44335 ADAR1 variants RNA-Seq This paper GEO: GSE285023 Original data files This paper https://doi.org/10.17632/r8zwszrjxj.1 Experimental models: Cell lines HEK293T cells ATCC ATTC# CRL-3216 Experimental models: Organisms/strains E. coli Stellar Competent Cells Takara Cat#636767 E. coli Rosetta 2(DE3) Competent Cells Novagen Cat#70954-4 Oligonucleotides DNA primers for cloning This paper Table S1 DNA oligos for IVT template This paper Table S2 RNAs This paper Table S3 rRNA depletion oligos Adiconis et al.65 N/A Recombinant DNA pmGFP-ADAR1-p150 Addgene Addgene plasmid #117927 Wild type pLEXm-ADAR1 and mutants This paper N/A pET-SUMO-EcEndoV This paper N/A pUC19 vector ThermoFisher Scientific Cat#SD0061 Software and algorithms AlphaFold2 in Google CoLab DeepMind and Google https://colab.research.google.com/ github/sokrypton/ColabFold/blob/ main/AlphaFold2.ipynb Relion version 4.0 Kimanius et al.66 https://www3.mrc-lmb.cam.ac.uk/ relion//index.php/Main_Page/; RRID:SCR_016274 MotionCorr2 Zheng et al.67 https://emcore.ucsf.edu/ucsf-software GCTF Zhang68 https://sbgrid.org/software/titles/gctf SerialEM Mastronarde et al.69 https://bio3d.colorado.edu/SerialEM/ Prism (GraphPad) Version 9.4.1 N/A www.graphpad.com cryoSPARC version 3.3 Punjani et al.70 https://cryosparc.com/; RRID:SCR_016501 UCSF Chimera Pettersen et al.71 https://www.cgl.ucsf.edu/chimera/; RRID:SCR_004097 PyMOL N/A https://www.pymol.org/pymol.html Phenix version 1.18.2 Afonine et al.72 https://www.phenix-online.org/; RRID:SCR_014224 Coot version 0.9.6 Emsley and Cowtan73 https://www2.mrc-lmb.cam.ac.uk/ personal/ pemsley/coot/; RRID:SCR_014222 pileup2var Xiao et al.74 https://github.com/shunliubio/pileup2var Other Quantifoil R 1.2/1.3 Cu grids EMS Cat#Q3100CR1.3 Au-Flat 1.2/1.3 AU grids EMS Cat#AUFT313-50 UltrAuFoil R 1.2/1.3 Au grids EMS Cat#Q350AR13A e2 Molecular Cell 85, 1381–1394.e1–e6, April 3, 2025 .. The HEK293T cell was established as an adherent cell line with the culture medium containing DMEM (ATCC, catalog 30-2002), 10% FBS (Thermo Fisher, catalog 16000044), and 1X L-Glutamine (ATCC, catalog 30-2214) in an incubator set at 37 C and 5% CO2, and the cells were then adapted to the suspension growth with suspension culture containing Freestyle medium (Thermo Fisher, catalog 12338026) and 1%FBSwhen the cells reached about 50% confluency.



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