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- PDB-1sva: SIMIAN VIRUS 40 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1sva
TitleSIMIAN VIRUS 40
ComponentsSIMIAN VIRUS 40SV40
KeywordsVIRUS / VIRUS COAT PROTEIN / Icosahedral virus
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 / structural molecule activity / virion attachment to host cell / identical protein binding
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
Major capsid protein VP1
Similarity search - Component
Biological speciesSimian virus 40
MethodX-RAY DIFFRACTION / Resolution: 3.1 Å
AuthorsStehle, T. / Gamblin, S.J. / Harrison, S.C.
Citation
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.
#1: Journal: Nature / Year: 1991
Title: Structure of Simian Virus 40 at 3.8-A Resolution
Authors: Liddington, R.C. / Yan, Y. / Moulai, J. / Sahli, R. / Benjamin, T.L. / Harrison, S.C.
History
DepositionNov 27, 1995Processing site: BNL
Revision 1.0Jun 10, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: SIMIAN VIRUS 40
2: SIMIAN VIRUS 40
3: SIMIAN VIRUS 40
4: SIMIAN VIRUS 40
5: SIMIAN VIRUS 40
6: SIMIAN VIRUS 40


Theoretical massNumber of molelcules
Total (without water)238,9146
Polymers238,9146
Non-polymers00
Water0
1
1: SIMIAN VIRUS 40
2: SIMIAN VIRUS 40
3: SIMIAN VIRUS 40
4: SIMIAN VIRUS 40
5: SIMIAN VIRUS 40
6: SIMIAN VIRUS 40
x 60


Theoretical massNumber of molelcules
Total (without water)14,334,829360
Polymers14,334,829360
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
1: SIMIAN VIRUS 40
2: SIMIAN VIRUS 40
3: SIMIAN VIRUS 40
4: SIMIAN VIRUS 40
5: SIMIAN VIRUS 40
6: SIMIAN VIRUS 40
x 5


  • icosahedral pentamer
  • 1.19 MDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)1,194,56930
Polymers1,194,56930
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: SIMIAN VIRUS 40
2: SIMIAN VIRUS 40
3: SIMIAN VIRUS 40
4: SIMIAN VIRUS 40
5: SIMIAN VIRUS 40
6: SIMIAN VIRUS 40
x 6


  • icosahedral 23 hexamer
  • 1.43 MDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)1,433,48336
Polymers1,433,48336
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
1: SIMIAN VIRUS 40
2: SIMIAN VIRUS 40
3: SIMIAN VIRUS 40
4: SIMIAN VIRUS 40
5: SIMIAN VIRUS 40
6: SIMIAN VIRUS 40
x 5


  • crystal asymmetric unit, crystal frame
  • 1.19 MDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)1,194,56930
Polymers1,194,56930
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation4
Unit cell
Length a, b, c (Å)558.000, 558.000, 558.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.30901699, -0.80901699, 0.5), (0.80901699, 0.5, 0.30901699), (-0.5, 0.30901699, 0.80901699)
3generate(-0.80901699, -0.5, 0.30901699), (0.5, -0.30901699, 0.80901699), (-0.30901699, 0.80901699, 0.5)
4generate(-0.80901699, 0.5, -0.30901699), (-0.5, -0.30901699, 0.80901699), (0.30901699, 0.80901699, 0.5)
5generate(0.30901699, 0.80901699, -0.5), (-0.80901699, 0.5, 0.30901699), (0.5, 0.30901699, 0.80901699)

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Components

#1: Protein
SIMIAN VIRUS 40 / SV40


Mass: 39818.969 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Simian virus 40 / Genus: PolyomavirusPolyomaviridae / References: UniProt: P03087

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal grow
*PLUS
Temperature: 25 ℃ / Method: vapor diffusion, hanging drop / PH range low: 7.5 / PH range high: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15-10 mg/mlvirus1drop
250 %satammonium sulfate1reservoir
310 mM1reservoirMn2+
40.5 mM1reservoirCa2+

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.1→12 Å / Num. obs: 402347 / % possible obs: 80.2 % / Observed criterion σ(I): 0
Reflection
*PLUS
Rmerge(I) obs: 0.097
Reflection shell
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 3.3 Å / % possible obs: 62.6 % / Num. unique obs: 54413 / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 1.6

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 3.1→12 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.268 --
Rwork0.257 --
obs0.257 402347 80.2 %
Refinement stepCycle: LAST / Resolution: 3.1→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15983 0 0 0 15983
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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