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Yorodumi- PDB-7c8p: Structural and functional characterization of human group A rotav... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7c8p | |||||||||
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Title | Structural and functional characterization of human group A rotavirus P[25] VP8* | |||||||||
Components | Outer capsid protein VP4 | |||||||||
Keywords | PROTEIN BINDING / human P[25] rotavirus / glycan binding specificity / VP8* / histo-blood group antigen (HBGA) | |||||||||
Function / homology | Function and homology information host cell rough endoplasmic reticulum / host cytoskeleton / viral outer capsid / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / virion attachment to host cell / host cell plasma membrane / membrane Similarity search - Function | |||||||||
Biological species | Rotavirus A | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | |||||||||
Authors | Duan, Z. / Dandi, L. | |||||||||
Funding support | China, 2items
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Citation | Journal: Virology / Year: 2021 Title: Human group A rotavirus P[25] VP8* specifically binds to A-type histo-blood group antigen. Authors: Li, D. / Wang, M. / Qi, J. / Zhang, Q. / Wang, H. / Pang, L. / Sun, X. / Duan, Z. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7c8p.cif.gz | 141.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7c8p.ent.gz | 109.8 KB | Display | PDB format |
PDBx/mmJSON format | 7c8p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7c8p_validation.pdf.gz | 433.3 KB | Display | wwPDB validaton report |
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Full document | 7c8p_full_validation.pdf.gz | 434.7 KB | Display | |
Data in XML | 7c8p_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 7c8p_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/7c8p ftp://data.pdbj.org/pub/pdb/validation_reports/c8/7c8p | HTTPS FTP |
-Related structure data
Related structure data | 4drvS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18463.637 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rotavirus A Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) References: UniProt: M1GR78 #2: 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: 5.02 Å3/Da / Density % sol: 75.48 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 2.0 M ammonium sulfate, 0.1 M sodium HEPES pH 7.5, and 2% v/v polyethylene glycol 400 |
-Data collection
Diffraction | Mean temperature: 118 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97774 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 16, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97774 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 23849 / % possible obs: 99.3 % / Redundancy: 8.6 % / Biso Wilson estimate: 43.79 Å2 / Rmerge(I) obs: 0.185 / Rsym value: 0.185 / Net I/σ(I): 11.968 |
Reflection shell | Resolution: 2.6→2.69 Å / Mean I/σ(I) obs: 3.077 / Num. unique obs: 23849 / Rsym value: 0.71 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DRV Resolution: 2.6→49.574 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.87 / Stereochemistry target values: ML
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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 max: 100.65 Å2 / Biso mean: 40.1347 Å2 / Biso min: 25.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.6→49.574 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | S33: 0 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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