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Open data
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Basic information
Entry | Database: PDB / ID: 7zlq | ||||||
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Title | Crystal structure of ADAR1-dsRBD3 dimer in complex with dsRNA | ||||||
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![]() | RNA BINDING PROTEIN / Editing / ADAR / RNA-binding domain | ||||||
Function / homology | ![]() 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 / negative regulation of hepatocyte apoptotic process / pre-miRNA processing / 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 / Interferon alpha/beta signaling / double-stranded RNA binding / 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 | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mboukou, A. / Barraud, P. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 136.3 KB | Display | ![]() |
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PDB format | ![]() | 93 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465.1 KB | Display | ![]() |
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Full document | ![]() | 467.6 KB | Display | |
Data in XML | ![]() | 9.1 KB | Display | |
Data in CIF | ![]() | 11.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7zj1SC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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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.) ![]() ![]() ![]() References: UniProt: P55265, double-stranded RNA adenine deaminase #2: RNA chain | Mass: 4132.518 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.04 Å3/Da / Density % sol: 69.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 50 mM sodium cacodylate, 5% (w/v) PEG 4000, 30 mM CaCl2, 230 mM KCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 12, 2019 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.8→44.58 Å / Num. obs: 10044 / % possible obs: 94.9 % / Redundancy: 19.2 % / Biso Wilson estimate: 37.91 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.038 / Rrim(I) all: 0.167 / Net I/σ(I): 16.6 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7ZJ1 Resolution: 2.8→44.58 Å / SU ML: 0.2653 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.3849 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: 80.97 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→44.58 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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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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