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- PDB-2snw: SINDBIS VIRUS CAPSID PROTEIN, TYPE3 CRYSTAL FORM -

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Basic information

Entry
Database: PDB / ID: 2snw
TitleSINDBIS VIRUS CAPSID PROTEIN, TYPE3 CRYSTAL FORM
ComponentsCOAT PROTEIN C
KeywordsVIRAL PROTEIN / SINDBIS / VIRUS / PROTEINASE / ALPHAVIRUS / CAPSID / CHYMOTRYPSIN / VIRUS 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 / viral translational frameshifting / serine-type endopeptidase activity ...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 / 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 / MIR, MOLECULAR REPLACEMENT AVERAGING BETWEEN TWO CRYSTAL FORMS / Resolution: 2.7 Å
AuthorsChoi, H.-K. / Lee, S. / Zhang, Y.-P. / Mckinney, B.R. / Wengler, G. / Rossmann, M.G. / Kuhn, R.J.
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: 1997
Title: Erratum. 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.
#2: 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.
#3: 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.
#4: 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.
#5: 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
DepositionFeb 17, 1998Processing site: BNL
SupersessionApr 8, 1998ID: 1SNW
Revision 1.0Apr 8, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COAT PROTEIN C
B: COAT PROTEIN C


Theoretical massNumber of molelcules
Total (without water)34,5752
Polymers34,5752
Non-polymers00
Water21612
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.800, 79.700, 60.800
Angle α, β, γ (deg.)90.00, 102.20, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.805227, 0.436695, 0.401132), (0.463269, -0.885561, 0.034111), (0.370123, 0.158365, -0.915385)
Vector: -7.9744, 13.8182, 21.9927)

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Components

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


Mass: 17287.484 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sindbis virus / Genus: Alphavirus / Cell line: BABY HAMSTER KIDNEY CELLS (BHK21) / Organ: KIDNEY / Strain: SA-AR 86
References: UniProt: P03316, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54 % / Description: THESE ARE RE-REFINED COORDINATES OF 1SNW.
Crystal growpH: 8.3 / Details: 6-8%(W/V) PEG 8000, 300 MM TRIS, PH8.3
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
13-4 mg/mlprotein1drop
23-4 %(w/v)PEG80001drop
325-150 mMTris-HCl1drop
46-8 %(w/v)PEG80001reservoir
550-300 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 285 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-20 / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Feb 1, 1992 / Details: BENT FOCUSING MIRROR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 7850 / % possible obs: 77.9 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Biso Wilson estimate: 42.5 Å2 / Rmerge(I) obs: 0.047
Reflection shellResolution: 2.6→2.8 Å / Rsym value: 0.169 / % possible all: 15.9
Reflection
*PLUS
Num. measured all: 19983
Reflection shell
*PLUS
% possible obs: 23.2 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
XDSdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR, MOLECULAR REPLACEMENT AVERAGING BETWEEN TWO CRYSTAL FORMS
Resolution: 2.7→8 Å / Data cutoff high absF: 1154 / Data cutoff low absF: 13 / σ(F): 1
RfactorNum. reflection% reflection
Rwork0.191 --
obs0.191 7445 78 %
Displacement parametersBiso mean: 33.7 Å2
Refine analyzeLuzzati d res low obs: 30 Å
Refinement stepCycle: LAST / Resolution: 2.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 0 12 2444
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_deg2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.7
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
Refine LS restraints NCSNCS model details: MOL1 AND MOL4, MOL2 AND MOL3 WERE RESTRAINED IN A PAIRWISE MANNER DURING REFINEMENT.
LS refinement shellResolution: 2.7→2.76 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rwork0.302 145 -
obs--22 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2TOPH19.PEP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.7

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