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Yorodumi- PDB-6umb: Crystal structure of TRIM7 B30.2 domain at 1.8 angstrom resolution -
+Open data
-Basic information
Entry | Database: PDB / ID: 6umb | ||||||
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Title | Crystal structure of TRIM7 B30.2 domain at 1.8 angstrom resolution | ||||||
Components | (E3 ubiquitin-protein ligase TRIM7) x 2 | ||||||
Keywords | LIGASE / B30.2 / E3 ubiquitin ligase / PRY/SPRY / TRIM7 | ||||||
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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Munoz Sosa, C.J. / Carrizo, M.E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2021 Title: Crystal structure and mutational analysis of the human TRIM7 B30.2 domain provide insights into the molecular basis of its binding to glycogenin-1. Authors: Munoz Sosa, C.J. / Issoglio, F.M. / Carrizo, M.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6umb.cif.gz | 88.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6umb.ent.gz | 65.5 KB | Display | PDB format |
PDBx/mmJSON format | 6umb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/um/6umb ftp://data.pdbj.org/pub/pdb/validation_reports/um/6umb | HTTPS FTP |
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-Related structure data
Related structure data | 6umaC 4n7iS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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: 20274.066 Da / Num. of mol.: 1 / Fragment: B30.2 domain 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 | Mass: 20197.947 Da / Num. of mol.: 1 / Fragment: B30.2 domain 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 | ||||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.25 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: Sodium malonate pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4586 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 16, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.4586 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→50.42 Å / Num. obs: 33860 / % possible obs: 99.6 % / Redundancy: 5.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.035 / Rrim(I) all: 0.084 / Net I/σ(I): 10.7 / Num. measured all: 193627 / Scaling rejects: 1069 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4N7I Resolution: 1.8→45.83 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.918 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.125 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 91.85 Å2 / Biso mean: 24.54 Å2 / Biso min: 7.54 Å2
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Refinement step | Cycle: final / Resolution: 1.8→45.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.804→1.851 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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