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- PDB-1vcp: SEMLIKI FOREST VIRUS CAPSID PROTEIN (CRYSTAL FORM I) -

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Basic information

Entry
Database: PDB / ID: 1vcp
TitleSEMLIKI FOREST VIRUS CAPSID PROTEIN (CRYSTAL FORM I)
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 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 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
C: SEMLIKI FOREST VIRUS CAPSID PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3596
Polymers48,7573
Non-polymers6023
Water00
1
A: SEMLIKI FOREST VIRUS CAPSID PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4532
Polymers16,2521
Non-polymers2011
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: SEMLIKI FOREST VIRUS CAPSID PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4532
Polymers16,2521
Non-polymers2011
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: SEMLIKI FOREST VIRUS CAPSID PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4532
Polymers16,2521
Non-polymers2011
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.140, 176.220, 40.210
Angle α, β, γ (deg.)90.00, 110.36, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.995376, 0.056591, -0.077609), (0.044604, -0.443259, -0.895283), (-0.085066, -0.894605, 0.438686)30.133, 154.179, 97.55
2given(0.921406, -0.240682, 0.305096), (0.12678, 0.928336, 0.349456), (-0.367339, -0.28331, 0.885888)28.657, -66.686, 7.486

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Components

#1: Protein SEMLIKI FOREST VIRUS CAPSID PROTEIN


Mass: 16252.439 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: CRYSTAL FORM 1 / Source: (gene. exp.) Semliki forest virus / Genus: Alphavirus / Organ: KIDNEY / Production host: Cricetinae gen. sp. (mammal) / References: UniProt: P03315
#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Hg

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.85 %
Crystal growDetails: KHGI4 WAS REQUIRED TO OBTAIN BIG CRYSTALS. EACH OF THREE MONOMERS OF THE SEMLIKI FOREST VIRUS CORE PROTEIN BIND ONE MERCURY ATOM. THE HG ATOM FORMS A S-HG-S BOND WITH CYS 119 AND CYS 134. IN ...Details: KHGI4 WAS REQUIRED TO OBTAIN BIG CRYSTALS. EACH OF THREE MONOMERS OF THE SEMLIKI FOREST VIRUS CORE PROTEIN BIND ONE MERCURY ATOM. THE HG ATOM FORMS A S-HG-S BOND WITH CYS 119 AND CYS 134. IN THE NATIVE STRUCTURE THERE IS A DISULFIDE BRIDGE BETWEEN CYS 119 AND CYS 134. THE S-HG DISTANCE WAS RESTRAINED TO 2.45 ANGSTROMS WHILE THE BOND ANGLE OF S-HG-S WAS RESTRAINED TO 180 DEGREES.
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 mMTris-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: 6747 / % possible obs: 66 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Rmerge(I) obs: 0.076
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 10 Å
Reflection shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.6 Å / % possible obs: 44.3 % / Num. unique obs: 1933 / Rmerge(I) obs: 0.118

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
X-PLORphasing
RefinementResolution: 3→6 Å / σ(F): 1
Details: RESIDUE ASP A 254 IS LOCATED IN GENEROUSLY ALLOWED REGIONS OF A RAMACHANDRAN PLOT. THE ELECTRON DENSITY OF THIS RESIDUE IS WELL DEFINED.
RfactorNum. reflection
Rwork0.157 -
obs0.157 5452
Displacement parametersBiso mean: 12.9 Å2
Refinement stepCycle: LAST / Resolution: 3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3426 0 3 0 3429
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
Solvent computation
*PLUS
Displacement parameters
*PLUS

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