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Yorodumi- PDB-2b4i: Crystal Structure of the Rhesus Rotavirus VP5 Antigen Domain Trimer -
+Open data
-Basic information
Entry | Database: PDB / ID: 2b4i | ||||||
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Title | Crystal Structure of the Rhesus Rotavirus VP5 Antigen Domain Trimer | ||||||
Components | Outer capsid protein VP4 | ||||||
Keywords | VIRAL PROTEIN / BETA SANDWICH / GREEK KEY / MEMBRANE PENETRATION PROTEIN / NON-ENVELOPED VIRUS / SPIKE PROTEIN / REARRANGEMENT | ||||||
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 | Rhesus rotavirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Yoder, J.D. / Dormitzer, P.R. | ||||||
Citation | Journal: Embo J. / Year: 2006 Title: Alternative intermolecular contacts underlie the rotavirus VP5(*) two- to three-fold rearrangement Authors: Yoder, J.D. / Dormitzer, P.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2b4i.cif.gz | 157.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b4i.ent.gz | 123.8 KB | Display | PDB format |
PDBx/mmJSON format | 2b4i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b4/2b4i ftp://data.pdbj.org/pub/pdb/validation_reports/b4/2b4i | HTTPS FTP |
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-Related structure data
Related structure data | 2b4hC 1slqS 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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Unit cell |
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-Components
#1: Protein | Mass: 28524.771 Da / Num. of mol.: 3 / Fragment: VP5* Antigen Domain Source method: isolated from a genetically manipulated source Details: see remark 400 / Source: (gene. exp.) Rhesus rotavirus / Species: Rotavirus A / Gene: GENOME SEGMENT 4 / Plasmid: pFastBac-1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: Q91HI9, UniProt: P12473*PLUS #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: 2.29 Å3/Da / Density % sol: 51.6 % |
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Crystal grow | Temperature: 281.15 K / Method: batch / pH: 8 Details: Tris, sodium chloride, EDTA, pH 8.0, Batch, temperature 281.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9998 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2004 |
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9998 Å / Relative weight: 1 |
Reflection | Resolution: 2→70 Å / Num. all: 55552 / Num. obs: 55552 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.71 % / Biso Wilson estimate: 35.06 Å2 / Rsym value: 0.047 / Net I/σ(I): 26.85 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 4.56 % / Mean I/σ(I) obs: 4.25 / Num. unique all: 3728 / Rsym value: 0.402 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Residues 267-470 of VP5CT (1SLQ) Resolution: 2→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 40.4061 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å
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