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Yorodumi- PDB-7vs9: Crystal structure of P domain from norovirus GI.9 capsid protein ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7vs9 | ||||||
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Title | Crystal structure of P domain from norovirus GI.9 capsid protein in complex with Lewis x antigen. | ||||||
Components | VP1 | ||||||
Keywords | VIRAL PROTEIN / norovirus / p-domain / capsid / histo blood group antigen | ||||||
Function / homology | Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Lewis X antigen, alpha anomer / VP1 Function and homology information | ||||||
Biological species | Norovirus Hu/GI/Vancouver730/2004/CAN | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.26 Å | ||||||
Authors | Murayama, K. / Kato-Murayama, M. / Shirouzu, M. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Febs Open Bio / Year: 2022 Title: Lewis fucose is a key moiety for the recognition of histo-blood group antigens by GI.9 norovirus, as revealed by structural analysis. Authors: Kimura-Someya, T. / Kato-Murayama, M. / Katsura, K. / Sakai, N. / Murayama, K. / Hanada, K. / Shirouzu, M. / Someya, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vs9.cif.gz | 147.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vs9.ent.gz | 112 KB | Display | PDB format |
PDBx/mmJSON format | 7vs9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vs/7vs9 ftp://data.pdbj.org/pub/pdb/validation_reports/vs/7vs9 | HTTPS FTP |
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-Related structure data
Related structure data | 7vp0SC 7vs8C 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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Unit cell |
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-Components
#1: Protein | Mass: 33777.852 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Norovirus Hu/GI/Vancouver730/2004/CAN / Details (production host): Cell-free protein synthesis / Production host: Escherichia coli (E. coli) / References: UniProt: F2XMU3 #2: Polysaccharide | #3: Chemical | #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 4.51 Å3/Da / Density % sol: 72.72 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: magnesium chloride, Bicine, pH 9.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 27, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→50 Å / Num. obs: 56256 / % possible obs: 99.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.088 / Rrim(I) all: 0.103 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 2.26→2.34 Å / Rmerge(I) obs: 0.349 / Num. unique obs: 5539 / Rrim(I) all: 0.411 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7VP0 Resolution: 2.26→35.207 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.87 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.26→35.207 Å
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Refine LS restraints |
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LS refinement shell |
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