+Open data
-Basic information
Entry | Database: PDB / ID: 7zj1 | ||||||
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Title | Crystal structure of ADAR1-dsRBD3 dimer | ||||||
Components | Double-stranded RNA-specific adenosine deaminase | ||||||
Keywords | RNA BINDING PROTEIN / Editing / ADAR / RNA-binding domain | ||||||
Function / homology | Function and homology information somatic diversification of immune receptors via somatic mutation / negative regulation of post-transcriptional gene silencing by regulatory ncRNA / C6 deamination of adenosine / Formation of editosomes by ADAR proteins / double-stranded RNA adenine deaminase / tRNA-specific adenosine deaminase activity / supraspliceosomal complex / double-stranded RNA adenosine deaminase activity / negative regulation of protein kinase activity by regulation of protein phosphorylation / base conversion or substitution editing ...somatic diversification of immune receptors via somatic mutation / negative regulation of post-transcriptional gene silencing by regulatory ncRNA / C6 deamination of adenosine / Formation of editosomes by ADAR proteins / double-stranded RNA adenine deaminase / tRNA-specific adenosine deaminase activity / supraspliceosomal complex / double-stranded RNA adenosine deaminase activity / negative regulation of protein kinase activity by regulation of protein phosphorylation / base conversion or substitution editing / hematopoietic stem cell homeostasis / response to interferon-alpha / adenosine to inosine editing / RISC complex assembly / pre-miRNA processing / negative regulation of hepatocyte apoptotic process / definitive hemopoiesis / negative regulation of type I interferon-mediated signaling pathway / hepatocyte apoptotic process / positive regulation of viral genome replication / RNA processing / hematopoietic progenitor cell differentiation / protein export from nucleus / erythrocyte differentiation / response to virus / PKR-mediated signaling / mRNA processing / cellular response to virus / osteoblast differentiation / protein import into nucleus / double-stranded RNA binding / Interferon alpha/beta signaling / defense response to virus / innate immune response / nucleolus / DNA binding / RNA binding / nucleoplasm / membrane / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å | ||||||
Authors | Mboukou, A. / Barraud, P. | ||||||
Funding support | France, 1items
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Citation | Journal: Biorxiv / Year: 2023 Title: Dimerization of ADAR1 modulates site-specificity of RNA editing Authors: Mboukou, A. / Rajendra, V. / Messmer, S. / Catala, M. / Tisne, C. / Jantsch, M.F. / Barraud, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zj1.cif.gz | 81.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zj1.ent.gz | 56.6 KB | Display | PDB format |
PDBx/mmJSON format | 7zj1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zj1_validation.pdf.gz | 427.3 KB | Display | wwPDB validaton report |
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Full document | 7zj1_full_validation.pdf.gz | 427.9 KB | Display | |
Data in XML | 7zj1_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | 7zj1_validation.cif.gz | 12.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zj/7zj1 ftp://data.pdbj.org/pub/pdb/validation_reports/zj/7zj1 | HTTPS FTP |
-Related structure data
Related structure data | 7zlqC 2mdrS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 9249.422 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ADAR, ADAR1, DSRAD, G1P1, IFI4 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P55265, double-stranded RNA adenine deaminase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 100 mM sodium citrate pH 4.0, 20% (w/v) PEG 6000, and 1.0 M LiCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 12, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.65→19.15 Å / Num. obs: 18792 / % possible obs: 99.26 % / Redundancy: 18.7 % / Biso Wilson estimate: 18.31 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.1518 / Rpim(I) all: 0.03536 / Rrim(I) all: 0.156 / Net I/σ(I): 12.45 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2MDR Resolution: 1.65→19.15 Å / SU ML: 0.1988 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.5923 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.45 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→19.15 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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