paper emdb emd 44335 adar1 variants rna seq Search Results


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
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wild type plexm adar1  (Addgene inc)
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Addgene inc wild type plexm adar1
Figure 3. Structural insights into ADAR1 editing (A) Structural comparison of the ADAR1-GLI and ADAR1-HT complex, with the monomer A aligned. The ADAR1-GLI complex and HT-V2 RNA in the ADAR1-HT complex are color coded as in Figures 2C and 2D, respectively. The ADAR1 dimer of the ADAR1-HT complex was colored in gray. (B and C) The zoom-in views of the RNA recognition site in ADAR1-GLI (B) and ADAR1-HT complexes (C). (D and E) Overview of the molecular interactions between ADAR1 and GLI-V11 (D) and HT-V2 (E) RNA. (F) Editing activity of ADAR1 <t>wild</t> <t>type</t> (WT) or mutants with different RNA substrates. Secondary structures of RNA substrates are displayed, with the editing site A highlighted in red.
Wild Type Plexm Adar1, supplied by Addgene inc, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Image Search Results


Figure 3. Structural insights into ADAR1 editing (A) Structural comparison of the ADAR1-GLI and ADAR1-HT complex, with the monomer A aligned. The ADAR1-GLI complex and HT-V2 RNA in the ADAR1-HT complex are color coded as in Figures 2C and 2D, respectively. The ADAR1 dimer of the ADAR1-HT complex was colored in gray. (B and C) The zoom-in views of the RNA recognition site in ADAR1-GLI (B) and ADAR1-HT complexes (C). (D and E) Overview of the molecular interactions between ADAR1 and GLI-V11 (D) and HT-V2 (E) RNA. (F) Editing activity of ADAR1 wild type (WT) or mutants with different RNA substrates. Secondary structures of RNA substrates are displayed, with the editing site A highlighted in red.

Journal: Molecular cell

Article Title: Biochemical profiling and structural basis of ADAR1-mediated RNA editing.

doi: 10.1016/j.molcel.2025.02.017

Figure Lengend Snippet: Figure 3. Structural insights into ADAR1 editing (A) Structural comparison of the ADAR1-GLI and ADAR1-HT complex, with the monomer A aligned. The ADAR1-GLI complex and HT-V2 RNA in the ADAR1-HT complex are color coded as in Figures 2C and 2D, respectively. The ADAR1 dimer of the ADAR1-HT complex was colored in gray. (B and C) The zoom-in views of the RNA recognition site in ADAR1-GLI (B) and ADAR1-HT complexes (C). (D and E) Overview of the molecular interactions between ADAR1 and GLI-V11 (D) and HT-V2 (E) RNA. (F) Editing activity of ADAR1 wild type (WT) or mutants with different RNA substrates. Secondary structures of RNA substrates are displayed, with the editing site A highlighted in red.

Article Snippet: 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

Techniques: Comparison, Activity Assay

Figure 4. Structural, biochemical characterization and RNA-seq analysis of ADAR1 AGS-associated mutations (A) Mapping of AGS-associated mutations onto the ADAR1-GLI complex. (B) Editing activity of ADAR1 AGS-associated mutants with different RNA substrates. Values represent the mean of three independent experiments, with error bars indicating standard deviation. 100 nM ADAR1 or mutants and 25 nM each RNA were used. (C) Heatmap of RNA editing rates for WT and AGS-associated ADAR1 mutants across 37 selected RNAs, as determined by RNA-seq. The name, for example, CCNI_971, indicates editing at position A971 in the CCNI mRNA. Among the tested groups, the G1007R mutant shows the most severe defects in RNA editing. (D) Editing activity of wild-type (WT) ADAR1 and AGS-associated mutants on selected dsRNAs identified from RNA-seq data. Secondary structures of the RNAs are shown, with the editing site adenosine (A) highlighted in red. The black dotted line indicates 10% editing activity as a reference. See also Figures S8 and S10.

Journal: Molecular cell

Article Title: Biochemical profiling and structural basis of ADAR1-mediated RNA editing.

doi: 10.1016/j.molcel.2025.02.017

Figure Lengend Snippet: Figure 4. Structural, biochemical characterization and RNA-seq analysis of ADAR1 AGS-associated mutations (A) Mapping of AGS-associated mutations onto the ADAR1-GLI complex. (B) Editing activity of ADAR1 AGS-associated mutants with different RNA substrates. Values represent the mean of three independent experiments, with error bars indicating standard deviation. 100 nM ADAR1 or mutants and 25 nM each RNA were used. (C) Heatmap of RNA editing rates for WT and AGS-associated ADAR1 mutants across 37 selected RNAs, as determined by RNA-seq. The name, for example, CCNI_971, indicates editing at position A971 in the CCNI mRNA. Among the tested groups, the G1007R mutant shows the most severe defects in RNA editing. (D) Editing activity of wild-type (WT) ADAR1 and AGS-associated mutants on selected dsRNAs identified from RNA-seq data. Secondary structures of the RNAs are shown, with the editing site adenosine (A) highlighted in red. The black dotted line indicates 10% editing activity as a reference. See also Figures S8 and S10.

Article Snippet: 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

Techniques: RNA Sequencing, Activity Assay, Standard Deviation, Mutagenesis