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- PDB-1svp: SINDBIS VIRUS CAPSID PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1svp
TitleSINDBIS VIRUS CAPSID PROTEIN
ComponentsSINDBIS VIRUS CAPSID PROTEIN
KeywordsVIRAL PROTEIN / SINDBIS VIRUS CAPSID PROTEIN / CHYMOTRYPSIN-LIKE SERINE / MUTANT / COAT PROTEIN
Function / homology
Function and homology information


icosahedral viral capsid, spike / togavirin / T=4 icosahedral viral capsid / ubiquitin-like protein ligase binding / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / membrane fusion / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane ...icosahedral viral capsid, spike / togavirin / T=4 icosahedral viral capsid / ubiquitin-like protein ligase binding / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / membrane fusion / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / 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 speciesSindbis virus
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsLee, S. / Rossmann, M.G.
Citation
Journal: Structure / Year: 1996
Title: Identification of a protein binding site on the surface of the alphavirus nucleocapsid and its implication in virus assembly.
Authors: Lee, S. / Owen, K.E. / Choi, H.K. / Lee, H. / Lu, G. / Wengler, G. / Brown, D.T. / Rossmann, M.G. / Kuhn, R.J.
#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: Acta Crystallogr.,Sect.A / Year: 1992
Title: The Structure Determination of Sindbis Virus Core Protein Using Isomorphous Replacement and Molecular Replacement Averaging between Two Crystal Forms
Authors: Tong, L. / Choi, H.-K. / Minor, W. / Rossmann, M.G.
#3: 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 22, 1996Processing site: BNL
Revision 1.0Aug 17, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SINDBIS VIRUS CAPSID PROTEIN
B: SINDBIS VIRUS CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)35,1222
Polymers35,1222
Non-polymers00
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.000, 56.500, 60.830
Angle α, β, γ (deg.)93.10, 96.73, 94.93
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.999566, 0.003141, -0.029297), (-0.010181, 0.96988, -0.243369), (0.02765, 0.243561, 0.969491)
Vector: 8.50972, 25.86226, 30.28011)

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Components

#1: Protein SINDBIS VIRUS CAPSID PROTEIN / SINDBIS VIRUS COAT PROTEIN


Mass: 17560.838 Da / Num. of mol.: 2
Fragment: MET 106 - ALA 264 OF THE NATIVE SINDBIS CAPSID PROTEIN
Mutation: DEL(1-105), S215A, INS(S265,A266)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sindbis virus / Genus: Alphavirus / Description: T7 RNA POLYMERASE / Gene: SINDBIS VIRUS CAPSID PROTEIN / Plasmid: PET11A / Gene (production host): SINDBIS VIRUS CAPSID PROTEIN / Production host: Escherichia coli (E. coli)
References: UniProt: P03316, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56 %
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Boege, U., (1989) J. Mol. Biol., 208, 79.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 %(w/v)PEG80001reservoir
2100-200 mMTris1reservoir
35-10 mg/mlprotein1drop
44 %(w/v)PEG80001drop
550-100 mMTris1drop

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 22, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 2.63 % / Rmerge(I) obs: 0.036

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementResolution: 2→5 Å / σ(F): 0
RfactorNum. reflection
Rfree0.279 -
Rwork0.184 -
obs0.184 15488
Displacement parametersBiso mean: 29.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2452 0 0 133 2585
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_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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