+Open data
-Basic information
Entry | Database: PDB / ID: 7x6z | ||||||
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Title | TRIM7 in complex with C-terminal peptide of NSP12 | ||||||
Components |
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Keywords | ANTIVIRAL PROTEIN | ||||||
Function / homology | Function and homology information antiviral innate immune response / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / protein ubiquitination / Golgi apparatus / zinc ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Severe acute respiratory syndrome coronavirus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.43 Å | ||||||
Authors | Zhang, H. / Liang, X. / Li, X.Z. | ||||||
Funding support | 1items
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Citation | Journal: Nat.Chem.Biol. / Year: 2022 Title: A C-terminal glutamine recognition mechanism revealed by E3 ligase TRIM7 structures. Authors: Liang, X. / Xiao, J. / Li, X. / Liu, Y. / Lu, Y. / Wen, Y. / Li, Z. / Che, X. / Ma, Y. / Zhang, X. / Zhang, Y. / Jian, D. / Wang, P. / Xuan, C. / Yu, G. / Li, L. / Zhang, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7x6z.cif.gz | 103.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7x6z.ent.gz | 65.7 KB | Display | PDB format |
PDBx/mmJSON format | 7x6z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x6/7x6z ftp://data.pdbj.org/pub/pdb/validation_reports/x6/7x6z | HTTPS FTP |
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-Related structure data
Related structure data | 7w0qC 7w0sC 7w0tC 7x6yC 7x70C C: citing same article (ref.) |
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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: 19689.295 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM7, GNIP, RNF90 / Production host: Escherichia coli (E. coli) References: UniProt: Q9C029, RING-type E3 ubiquitin transferase |
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#2: Protein/peptide | Mass: 694.798 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Severe acute respiratory syndrome coronavirus 2 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.11 % |
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Crystal grow | Temperature: 291.15 K / Method: liquid diffusion / Details: DL-Malic acid, PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 6, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→26.2 Å / Num. obs: 35358 / % possible obs: 98.22 % / Redundancy: 2 % / Biso Wilson estimate: 15.68 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.56 |
Reflection shell | Resolution: 1.43→1.48 Å / Num. unique obs: 6895 / CC1/2: 0.829 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.43→26.2 Å / SU ML: 0.1394 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.4205 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.16 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.43→26.2 Å
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Refine LS restraints |
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LS refinement shell |
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