[English] 日本語
Yorodumi- PDB-6h9y: Unraveling the role of the secretor antigen in human rotavirus at... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6h9y | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Unraveling the role of the secretor antigen in human rotavirus attachment to histo-blood group antigens | |||||||||
Components | Outer capsid protein VP4 | |||||||||
Keywords | VIRAL PROTEIN / histo-blood group antigen rotavirus | |||||||||
Function / homology | Function and homology information 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 / host cell membrane / viral capsid / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / membrane Similarity search - Function | |||||||||
Biological species | Human rotavirus A | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å | |||||||||
Authors | Ciges-Tomas, J.R. / Gozalbo-Rovira, R. / Vila-Vicent, S. / Buesa, J. / Santiso-Bellon, C. / Monedero, V. / Yebra, M.J. / Rodriguez-Diaz, J. / Marina, A. | |||||||||
Funding support | Spain, 1items
| |||||||||
Citation | Journal: Plos Pathog. / Year: 2019 Title: Unraveling the role of the secretor antigen in human rotavirus attachment to histo-blood group antigens. Authors: Gozalbo-Rovira, R. / Ciges-Tomas, J.R. / Vila-Vicent, S. / Buesa, J. / Santiso-Bellon, C. / Monedero, V. / Yebra, M.J. / Marina, A. / Rodriguez-Diaz, J. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6h9y.cif.gz | 93.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6h9y.ent.gz | 68 KB | Display | PDB format |
PDBx/mmJSON format | 6h9y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6h9y_validation.pdf.gz | 830 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6h9y_full_validation.pdf.gz | 832.1 KB | Display | |
Data in XML | 6h9y_validation.xml.gz | 20 KB | Display | |
Data in CIF | 6h9y_validation.cif.gz | 31.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h9/6h9y ftp://data.pdbj.org/pub/pdb/validation_reports/h9/6h9y | HTTPS FTP |
-Related structure data
Related structure data | 6h9wSC 6h9zC 6ha0C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18550.332 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: G1 and S2 are residuals from tag digestion / Source: (gene. exp.) Human rotavirus A / Gene: VP4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2K9UWM4, UniProt: Q0PRF2*PLUS #2: Polysaccharide | beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-BTB / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 35.95 % |
---|---|
Crystal grow | Temperature: 294.15 K / Method: vapor diffusion, sitting drop / Details: 1.5M Li2SO4 0.1M Tris pH6.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97907 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2017 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97907 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.31→66.79 Å / Num. obs: 64030 / % possible obs: 94.9 % / Redundancy: 3.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.053 / Rrim(I) all: 0.102 / Net I/σ(I): 8.4 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6H9W Resolution: 1.31→66.79 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU R Cruickshank DPI: 0.0633 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.065 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.69 Å2 / Biso mean: 12.386 Å2 / Biso min: 5.64 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.31→66.79 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.31→1.344 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|