+Open data
-Basic information
Entry | Database: PDB / ID: 8a8x | ||||||
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Title | TRIM7 PRYSPRY in complex with a MNV1-NS3 peptide HDDFGLQ | ||||||
Components |
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Keywords | PROTEIN BINDING / TRIM / LIGASE / PRYSPRY | ||||||
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) Murine norovirus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å | ||||||
Authors | Luptak, J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Viruses / Year: 2022 Title: TRIM7 Restricts Coxsackievirus and Norovirus Infection by Detecting the C-Terminal Glutamine Generated by 3C Protease Processing. Authors: Luptak, J. / Mallery, D.L. / Jahun, A.S. / Albecka, A. / Clift, D. / Ather, O. / Slodkowicz, G. / Goodfellow, I. / James, L.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8a8x.cif.gz | 148.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8a8x.ent.gz | 113.5 KB | Display | PDB format |
PDBx/mmJSON format | 8a8x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a8/8a8x ftp://data.pdbj.org/pub/pdb/validation_reports/a8/8a8x | HTTPS FTP |
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-Related structure data
Related structure data | 8a5lSC 8a5mC S: Starting model for refinement 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 20335.057 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM7, GNIP, RNF90 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 References: UniProt: Q9C029, RING-type E3 ubiquitin transferase #2: Protein/peptide | Mass: 831.850 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Murine norovirus 1 #3: 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: 2.3 Å3/Da / Density % sol: 46.6 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 1 M DL-Malic Acid pH 5, 0.1 M BIS-TRIS Propane pH 6.3 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 14, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.37→70.91 Å / Num. obs: 15418 / % possible obs: 97.4 % / Redundancy: 3.3 % / CC1/2: 1 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2.37→2.43 Å / Num. unique obs: 712 / CC1/2: 0.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8A5L Resolution: 2.37→28.337 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.899 / SU B: 10.12 / SU ML: 0.23 / Cross valid method: FREE R-VALUE / ESU R: 0.434 / ESU R Free: 0.283 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.428 Å2
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Refinement step | Cycle: LAST / Resolution: 2.37→28.337 Å
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Refine LS restraints |
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LS refinement shell |
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