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- PDB-1cn3: INTERACTION OF POLYOMAVIRUS INTERNAL PROTEIN VP2 WITH MAJOR CAPSI... -

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Basic information

Entry
Database: PDB / ID: 1cn3
TitleINTERACTION OF POLYOMAVIRUS INTERNAL PROTEIN VP2 WITH MAJOR CAPSID PROTEIN VP1 AND IMPLICATIONS FOR PARTICIPATION OF VP2 IN VIRAL ENTRY
Components
  • COAT PROTEIN VP1
  • FRAGMENT OF COAT PROTEIN VP2
KeywordsVIRAL PROTEIN / VIRAL COAT PROTEIN VP1 / VIRAL COAT PROTEIN VP2 / VIRAL ENTRY
Function / homology
Function and homology information


caveolin-mediated endocytosis of virus by host cell / T=7 icosahedral viral capsid / viral penetration into host nucleus / viral capsid / membrane => GO:0016020 / host cell endoplasmic reticulum membrane / symbiont entry into host cell / host cell nucleus / virion attachment to host cell / structural molecule activity / DNA binding
Similarity search - Function
Polyomavirus coat protein VP2 / Polyomavirus coat protein / 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
Minor capsid protein VP2 / Capsid protein VP1
Similarity search - Component
Biological speciesPolyomavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsChen, X. / Stehle, T. / Harrison, S.C.
CitationJournal: EMBO J. / Year: 1998
Title: Interaction of polyomavirus internal protein VP2 with the major capsid protein VP1 and implications for participation of VP2 in viral entry.
Authors: Chen, X.S. / Stehle, T. / Harrison, S.C.
History
DepositionMay 24, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jun 9, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: COAT PROTEIN VP1
B: COAT PROTEIN VP1
C: COAT PROTEIN VP1
D: COAT PROTEIN VP1
E: COAT PROTEIN VP1
F: FRAGMENT OF COAT PROTEIN VP2


Theoretical massNumber of molelcules
Total (without water)160,3056
Polymers160,3056
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24740 Å2
ΔGint-149 kcal/mol
Surface area52860 Å2
MethodPISA
2
A: COAT PROTEIN VP1
B: COAT PROTEIN VP1
C: COAT PROTEIN VP1
D: COAT PROTEIN VP1
E: COAT PROTEIN VP1
F: FRAGMENT OF COAT PROTEIN VP2

A: COAT PROTEIN VP1
B: COAT PROTEIN VP1
C: COAT PROTEIN VP1
D: COAT PROTEIN VP1
E: COAT PROTEIN VP1
F: FRAGMENT OF COAT PROTEIN VP2


Theoretical massNumber of molelcules
Total (without water)320,61012
Polymers320,61012
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
Buried area51720 Å2
ΔGint-312 kcal/mol
Surface area103480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)219.000, 219.000, 99.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Cell settingtrigonal
Space group name H-MP3121

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Components

#1: Protein
COAT PROTEIN VP1


Mass: 31501.611 Da / Num. of mol.: 5 / Fragment: RESIDUES 35-317
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Polyomavirus / Genus: PolyomavirusPolyomaviridae
Production host: Erinaceus europaeus (western European hedgehog)
References: UniProt: P49302
#2: Protein/peptide FRAGMENT OF COAT PROTEIN VP2


Mass: 2797.157 Da / Num. of mol.: 1 / Fragment: RESIDUES 279-297 / Source method: obtained synthetically / Details: sequence from COAT PROTEIN VP2 / References: UniProt: P12908

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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: 4.27 Å3/Da / Density % sol: 71.21 %
Crystal growpH: 4 / Details: pH 4.0
Crystal grow
*PLUS
pH: 8.4 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 %PEG60001reservoir
20.5 Mammonium sulfate1reservoir
310 mMdithiothreitol1reservoir
410 %glycerol1reservoir
50.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.98
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. obs: 25000 / % possible obs: 95 % / Observed criterion σ(I): 1.5 / Redundancy: 2.5 % / Rmerge(I) obs: 0.09 / Rsym value: 0.15

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 1.5
RfactorNum. reflection% reflectionSelection details
Rfree0.26 --RANDOM
Rwork0.23 ---
obs-25000 95 %-
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11261 0 0 0 11261
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
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_deg1.2
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

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