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- PDB-1vcq: SEMLIKI FOREST VIRUS CAPSID PROTEIN (CRYSTAL FORM II) -

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Basic information

Entry
Database: PDB / ID: 1vcq
TitleSEMLIKI FOREST VIRUS CAPSID PROTEIN (CRYSTAL FORM II)
ComponentsSEMLIKI FOREST VIRUS CAPSID PROTEIN
KeywordsVIRAL PROTEIN / VIRUS COAT PROTEIN / POLYPROTEIN / TRANSMEMBRANE / GLYCOPROTEIN / NUCLEOCAPSID PROTEIN
Function / homology
Function and homology information


togavirin / T=4 icosahedral viral capsid / virion assembly / small molecule binding / host cell endosome / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / viral translational frameshifting / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane ...togavirin / T=4 icosahedral viral capsid / virion assembly / small molecule binding / host cell endosome / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / viral translational frameshifting / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / RNA binding / membrane
Similarity search - Function
Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein ...Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein / Alphavirus E1 glycoprotein / Alphavirus core protein (CP) domain profile. / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Structural polyprotein
Similarity search - Component
Biological speciesSemliki forest virus
MethodX-RAY DIFFRACTION / Resolution: 3.1 Å
AuthorsLu, G. / Choi, H.-K. / Rossmann, M.G.
Citation
Journal: Proteins / Year: 1997
Title: Structure of Semliki Forest virus core protein.
Authors: Choi, H.K. / Lu, G. / Lee, S. / Wengler, G. / Rossmann, M.G.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Refined Structure of Sindbis Virus Core Protein and Comparison with Other Chymotrypsin-Like Serine Proteinase Structures
Authors: Tong, L. / Wengler, G. / Rossmann, M.G.
#2: Journal: Nature / Year: 1991
Title: Structure of Sindbis Virus Core Protein Reveals a Chymotrypsin-Like Serine Proteinase and the Organization of the Virion
Authors: Choi, H.K. / Tong, L. / Minor, W. / Dumas, P. / Boege, U. / Rossmann, M.G. / Wengler, G.
History
DepositionMar 4, 1996Processing site: BNL
Revision 1.0Dec 7, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: SEMLIKI FOREST VIRUS CAPSID PROTEIN
B: SEMLIKI FOREST VIRUS CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)32,5052
Polymers32,5052
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.717, 48.572, 70.372
Angle α, β, γ (deg.)90.00, 105.77, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.98386, -0.178791, -0.007245), (-0.178308, 0.982987, -0.044068), (0.015, -0.042065, -0.999002)
Vector: 16.276, 2.142, 33.404)

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Components

#1: Protein SEMLIKI FOREST VIRUS CAPSID PROTEIN


Mass: 16252.439 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CRYSTAL FORM II / Source: (gene. exp.) Semliki forest virus / Genus: Alphavirus / Organ: KIDNEY / Production host: Cricetinae gen. sp. (mammal) / References: UniProt: P03315
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.73 %
Crystal grow
*PLUS
pH: 8.3 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
25 mM1dropK2HgI4
33-5 %(w/v)PEG80001drop
4100-150 %(w/v)Tris-HCl1drop
56-10 %(w/v)PEG80001reservoir
6200-300 mMTris-HCl1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 5222 / % possible obs: 80.3 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.093
Reflection
*PLUS
Highest resolution: 3.3 Å / Lowest resolution: 10 Å
Reflection shell
*PLUS
Highest resolution: 3.3 Å / Lowest resolution: 3.6 Å / % possible obs: 80.7 % / Num. unique obs: 1286 / Rmerge(I) obs: 0.093

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Processing

Software
NameClassification
XDSdata scaling
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
X-PLORphasing
RefinementResolution: 3.1→6.5 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.157 -
obs0.157 4501
Displacement parametersBiso mean: 18.6 Å2
Refinement stepCycle: LAST / Resolution: 3.1→6.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2284 0 3 0 2287
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.7
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_d1.5
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.3
X-RAY DIFFRACTIONx_mcangle_it1.7
X-RAY DIFFRACTIONx_scbond_it1.5
X-RAY DIFFRACTIONx_scangle_it2.1
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.3 Å / Rfactor obs: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS

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