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- PDB-2snv: THE REFINED STRUCTURE OF SINDBIS VIRUS CORE PROTEIN IN COMPARISON... -

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Basic information

Entry
Database: PDB / ID: 2snv
TitleTHE REFINED STRUCTURE OF SINDBIS VIRUS CORE PROTEIN IN COMPARISON WITH OTHER CHYMOTRYPSIN-LIKE SERINE PROTEINASE STRUCTURES
ComponentsSINDBIS VIRUS COAT PROTEIN
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


icosahedral viral capsid, spike / togavirin / T=4 icosahedral viral capsid / ubiquitin-like protein ligase binding / clathrin-dependent endocytosis of virus by host cell / symbiont-mediated suppression of host toll-like receptor signaling pathway / membrane fusion / host cell cytoplasm / viral translational frameshifting / serine-type endopeptidase activity ...icosahedral viral capsid, spike / togavirin / T=4 icosahedral viral capsid / ubiquitin-like protein ligase binding / clathrin-dependent endocytosis of virus by host cell / symbiont-mediated suppression of host toll-like receptor signaling pathway / membrane fusion / host cell cytoplasm / 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 speciesSindbis virus
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsTong, L. / Rossmann, M.G.
Citation
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.
#1: 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.
#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
DepositionJul 17, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Remark 700SHEET THE STRAND ASSIGNMENTS OF THE SHEET RECORDS ARE TENTATIVE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SINDBIS VIRUS COAT PROTEIN


Theoretical massNumber of molelcules
Total (without water)16,5461
Polymers16,5461
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)57.000, 57.000, 109.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein SINDBIS VIRUS COAT PROTEIN


Mass: 16545.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sindbis virus / Genus: Alphavirus / References: UniProt: P03316

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.34 %
Crystal grow
*PLUS
pH: 8.3 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15-10 mg/mlprotein1drop
2200 mMTris-HCl1reservoir
38 %(w/v)PEG80001reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 3779 / Num. measured all: 17265 / Rmerge(I) obs: 0.063

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.2 / Rfactor obs: 0.2 / Highest resolution: 2.8 Å
Refinement stepCycle: LAST / Highest resolution: 2.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1164 0 0 0 1164
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.024
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_deg3.1
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
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 6 Å / Num. reflection obs: 3229 / Rfactor obs: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d3.1
X-RAY DIFFRACTIONx_dihedral_angle_d3.4
X-RAY DIFFRACTIONx_chiral_restr0.091

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