+Open data
-Basic information
Entry | Database: PDB / ID: 1vpn | ||||||
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Title | UNASSEMBLED POLYOMAVIRUS VP1 PENTAMER | ||||||
Components | POLYOMAVIRUS VP1 PENTAMER | ||||||
Keywords | VIRAL PROTEIN / VIRUS COAT PROTEIN / VIRUS ASSEMBLY | ||||||
Function / homology | Function and homology information caveolin-mediated endocytosis of virus by host cell / T=7 icosahedral viral capsid / host cell nucleus / virion attachment to host cell / structural molecule activity Similarity search - Function | ||||||
Biological species | Murine polyomavirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Stehle, T. / Harrison, S.C. | ||||||
Citation | Journal: Embo J. / Year: 1997 Title: High-resolution structure of a polyomavirus VP1-oligosaccharide complex: implications for assembly and receptor binding. Authors: Stehle, T. / Harrison, S.C. #1: Journal: Structure / Year: 1996 Title: The Structure of Simian Virus 40 Refined at 3.1 A Resolution Authors: Stehle, T. / Gamblin, S.J. / Yan, Y. / Harrison, S.C. #2: Journal: Structure / Year: 1996 Title: Crystal Structures of Murine Polyomavirus in Complex with Straight-Chain and Branched-Chain Sialyloligosaccharide Receptor Fragments Authors: Stehle, T. / Harrison, S.C. #3: Journal: Nature / Year: 1994 Title: Structure of Murine Polyomavirus Complexed with an Oligosaccharide Receptor Fragment Authors: Stehle, T. / Yan, Y. / Benjamin, T.L. / Harrison, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vpn.cif.gz | 328.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vpn.ent.gz | 266.2 KB | Display | PDB format |
PDBx/mmJSON format | 1vpn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vpn_validation.pdf.gz | 455.7 KB | Display | wwPDB validaton report |
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Full document | 1vpn_full_validation.pdf.gz | 467.7 KB | Display | |
Data in XML | 1vpn_validation.xml.gz | 73.8 KB | Display | |
Data in CIF | 1vpn_validation.cif.gz | 113.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vp/1vpn ftp://data.pdbj.org/pub/pdb/validation_reports/vp/1vpn | HTTPS FTP |
-Related structure data
Related structure data | 1vpsC 1sidS 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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2 |
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Unit cell |
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Details | THE COORDINATE SET CONSISTS OF FIVE VP1 MOLECULES THAT FORM A PENTAMER. |
-Components
#1: Protein | Mass: 32087.213 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Murine polyomavirus / Genus: Polyomavirus / Production host: Escherichia coli (E. coli) / References: UniProt: P49302 #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: 4.4 Å3/Da / Density % sol: 65 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 Details: DROP: 1.0 M AMMONIUM PHOSPHATE PH 8.0 2.5 & ETHANOL 8-10 MG/ML PROTEIN RESERVOIR: 2.0 M AMMONIUM PHOSPHATE PH 8.0 5 % ETHANOL | ||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 65 % | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Dec 1, 1994 / Details: MIRROR |
Radiation | Monochromator: WIGGLER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. obs: 172107 / % possible obs: 83.2 % / Observed criterion σ(I): 0 / Rsym value: 0.106 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 2→2.1 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.302 / % possible all: 62.2 |
Reflection | *PLUS Rmerge(I) obs: 0.106 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: POLYOMAVIRUS VP1 PENTAMER (PDB ENTRY 1SID) Resolution: 2→20 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 29.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.15 Å / Luzzati d res low obs: 20 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: UNRESTRAINED | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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