+Open data
-Basic information
Entry | Database: PDB / ID: 3bwr | |||||||||
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Title | SV40 VP1 pentamer in complex with GM1 oligosaccharide | |||||||||
Components | Capsid protein VP1 | |||||||||
Keywords | VIRAL PROTEIN / SV40 / GM1 / viral receptor / viral attachment / ganglioside / VP1 / polyomaviruses / Capsid protein / Late protein / Nucleus / Virion | |||||||||
Function / homology | Function and homology information capsomere / caveolin-mediated endocytosis of virus by host cell / viral capsid assembly / T=7 icosahedral viral capsid / host cell endoplasmic reticulum / molecular adaptor activity / host cell nucleus / virion attachment to host cell / structural molecule activity / identical protein binding Similarity search - Function | |||||||||
Biological species | Simian virus 40 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | |||||||||
Authors | Neu, U. / Stehle, T. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008 Title: Structural basis of GM1 ganglioside recognition by simian virus 40. Authors: Neu, U. / Woellner, K. / Gauglitz, G. / Stehle, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bwr.cif.gz | 285 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bwr.ent.gz | 230.2 KB | Display | PDB format |
PDBx/mmJSON format | 3bwr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bw/3bwr ftp://data.pdbj.org/pub/pdb/validation_reports/bw/3bwr | HTTPS FTP |
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-Related structure data
Related structure data | 3bwqC 1svaS 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: 29734.420 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Simian virus 40 / Genus: PolyomavirusPolyomaviridae / Gene: VP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03087 #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | Nonpolymer details | AUTHORS STATE THAT ALTHOUGH MODELED AS BETA, O1 OF GLC302 EXHIBITS INTERCHANGING ALPHA AND BETA ...AUTHORS STATE THAT ALTHOUGH MODELED AS BETA, O1 OF GLC302 EXHIBITS INTERCHANG | |
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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: 2.74 Å3/Da / Density % sol: 55.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: RESERVOIR: 0.1 M TRIS, PH 8.5, 24% PEG3350. DROP: RESERVOIR MIXED 4:1 WITH 30% ETHYLENE GLYCOL. THIS WAS MIXED 1:1 WITH VP1 (11 MG/ML), VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 29, 2006 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→30 Å / Num. obs: 68387 / % possible obs: 89.8 % / Redundancy: 8.7 % / Biso Wilson estimate: 33.9 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 1.9 / Num. unique all: 4050 / % possible all: 53.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SVA Resolution: 2.25→29.76 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.883 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.376 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: some of the residues from Gly30 to Asp42 were disordered in several chains and were not modeled. The side chain of Asp42 of chain E was modeled as Ala due to missing density.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.589 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→29.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.308 Å / Total num. of bins used: 20
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