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- PDB-1vpn: UNASSEMBLED POLYOMAVIRUS VP1 PENTAMER -

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Basic information

Entry
Database: PDB / ID: 1vpn
TitleUNASSEMBLED POLYOMAVIRUS VP1 PENTAMER
ComponentsPOLYOMAVIRUS VP1 PENTAMER
KeywordsVIRAL 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
Capsid protein VP1,Polyomavirus / Polyomavirus Vp1; Chain A / Capsid protein VP1,Polyomavirus / Polyomavirus capsid protein VP1 superfamily / Polyomavirus coat protein / Double-stranded DNA virus, group I, capsid / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMurine polyomavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsStehle, 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
DepositionMar 7, 1997Processing site: BNL
Revision 1.0May 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: POLYOMAVIRUS VP1 PENTAMER
B: POLYOMAVIRUS VP1 PENTAMER
C: POLYOMAVIRUS VP1 PENTAMER
D: POLYOMAVIRUS VP1 PENTAMER
E: POLYOMAVIRUS VP1 PENTAMER


Theoretical massNumber of molelcules
Total (without water)160,4365
Polymers160,4365
Non-polymers00
Water37,7592096
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22610 Å2
ΔGint-134 kcal/mol
Surface area54000 Å2
MethodPISA
2
A: POLYOMAVIRUS VP1 PENTAMER
B: POLYOMAVIRUS VP1 PENTAMER
C: POLYOMAVIRUS VP1 PENTAMER
D: POLYOMAVIRUS VP1 PENTAMER
E: POLYOMAVIRUS VP1 PENTAMER

A: POLYOMAVIRUS VP1 PENTAMER
B: POLYOMAVIRUS VP1 PENTAMER
C: POLYOMAVIRUS VP1 PENTAMER
D: POLYOMAVIRUS VP1 PENTAMER
E: POLYOMAVIRUS VP1 PENTAMER


Theoretical massNumber of molelcules
Total (without water)320,87210
Polymers320,87210
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_674x-y+1,-y+2,-z-1/31
Buried area47920 Å2
ΔGint-286 kcal/mol
Surface area105310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)221.500, 221.500, 99.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsTHE COORDINATE SET CONSISTS OF FIVE VP1 MOLECULES THAT FORM A PENTAMER.

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Components

#1: Protein
POLYOMAVIRUS VP1 PENTAMER


Mass: 32087.213 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murine polyomavirus / Genus: PolyomavirusPolyomaviridae / Production host: Escherichia coli (E. coli) / References: UniProt: P49302
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2096 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.4 Å3/Da / Density % sol: 65 %
Crystal growpH: 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
IDConc.Common nameCrystal-IDSol-ID
11.0 Mammonium phosphate1drop
22.5 %ethanol1drop
38-10 mg/mlprotein1drop
42.0 Mammonium phosphate1reservoir
55 %ethanol1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Dec 1, 1994 / Details: MIRROR
RadiationMonochromator: WIGGLER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: POLYOMAVIRUS VP1 PENTAMER (PDB ENTRY 1SID)

1sid


Resolution: 2→20 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.199 -2 %RANDOM
Rwork0.176 ---
obs0.176 172107 83.2 %-
Displacement parametersBiso mean: 29.9 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å / Luzzati d res low obs: 20 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11134 0 0 2096 13230
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.36
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: UNRESTRAINED
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL

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