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Open data
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Basic information
Entry | Database: PDB / ID: 7x6y | ||||||
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Title | TRIM7 in complex with C-terminal peptide of NSP5 | ||||||
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![]() | ANTIVIRAL PROTEIN | ||||||
Function / homology | ![]() 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 | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, H. / Liang, X. / Li, X.Z. | ||||||
Funding support | 1items
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![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 104.4 KB | Display | ![]() |
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PDB format | ![]() | 65.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.1 KB | Display | ![]() |
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Full document | ![]() | 433.2 KB | Display | |
Data in XML | ![]() | 11.1 KB | Display | |
Data in CIF | ![]() | 15.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7w0qSC ![]() 7w0sC ![]() 7w0tC ![]() 7x6zC ![]() 7x70C 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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Components
#1: Protein | Mass: 19689.295 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9C029, RING-type E3 ubiquitin transferase |
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#2: Protein/peptide | Mass: 740.825 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.64 % |
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Crystal grow | Temperature: 291.15 K / Method: liquid diffusion / Details: Potassium sodium tartrate tetrahydrate, Tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 1.39→26.16 Å / Num. obs: 39139 / % possible obs: 99.96 % / Redundancy: 2 % / Biso Wilson estimate: 13.37 Å2 / CC1/2: 0.997 / Net I/σ(I): 11.44 |
Reflection shell | Resolution: 1.39→1.44 Å / Num. unique obs: 3870 / CC1/2: 0.874 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7W0Q Resolution: 1.39→26.16 Å / SU ML: 0.1091 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.3592 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: 19.17 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.39→26.16 Å
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Refine LS restraints |
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LS refinement shell |
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