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- PDB-1kxf: SINDBIS VIRUS CAPSID, (WILD-TYPE) RESIDUES 1-264, TETRAGONAL CRYS... -

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Basic information

Entry
Database: PDB / ID: 1kxf
TitleSINDBIS VIRUS CAPSID, (WILD-TYPE) RESIDUES 1-264, TETRAGONAL CRYSTAL FORM (FORM II)
ComponentsSINDBIS VIRUS CAPSID PROTEIN
KeywordsVIRAL PROTEIN / SINDBIS VIRUS CAPSID PROTEIN / CHYMOTRYPSIN-LIKE SERINE PROTEINASE / WILD TYPE / VIRUS CAPSID 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 / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / 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: 2.38 Å
AuthorsChoi, H.-K. / Rossmann, M.G.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Structural analysis of Sindbis virus capsid mutants involving assembly and catalysis.
Authors: Choi, H.K. / Lee, S. / Zhang, Y.P. / McKinney, B.R. / Wengler, G. / 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
DepositionMay 5, 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 1.3Oct 12, 2016Group: Structure summary
Revision 1.4Feb 14, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SINDBIS VIRUS CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)17,4191
Polymers17,4191
Non-polymers00
Water28816
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 CAPSID PROTEIN / SINDBIS VIRUS CORE PROTEIN


Mass: 17418.680 Da / Num. of mol.: 1 / Fragment: MET 1 - ALA 264 OF THE NATIVE SINDBIS CAPSID
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sindbis virus / Genus: Alphavirus / Organ: KIDNEY / Production host: Cricetinae (hamsters)
References: UniProt: P03316, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Sequence detailscrystallized construct 1-264 was possibly cleaved during crystallization somewhere before residue ...crystallized construct 1-264 was possibly cleaved during crystallization somewhere before residue 106. The entry was annotated as 106-264 fragment

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.95 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 8.5 / PH range high: 7.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14.5-7.5 mg/mlprotein1drop
26-8 %(w/v)PEG80001reservoir
350-300 mMTris-HCl1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Feb 26, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.38 Å / Num. obs: 7908 / % possible obs: 96.2 % / Observed criterion σ(I): 1 / Redundancy: 2.42 % / Rmerge(I) obs: 0.042
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 9999 Å / Num. measured all: 19176
Reflection shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.6 Å / % possible obs: 90.4 % / Rmerge(I) obs: 0.134

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.38→6 Å / σ(F): 2
RfactorNum. reflection
Rfree0.284 -
Rwork0.19 -
obs0.19 6383
Displacement parametersBiso mean: 28.4 Å2
Refinement stepCycle: LAST / Resolution: 2.38→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1224 0 0 16 1240
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg1.8
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg27.5
X-RAY DIFFRACTIONx_improper_angle_deg1.6

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