+Open data
-Basic information
Entry | Database: PDB / ID: 1svp | ||||||
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Title | SINDBIS VIRUS CAPSID PROTEIN | ||||||
Components | SINDBIS VIRUS CAPSID PROTEIN | ||||||
Keywords | VIRAL 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 | ||||||
Biological species | Sindbis virus | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Lee, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1svp.cif.gz | 91.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1svp.ent.gz | 69.7 KB | Display | PDB format |
PDBx/mmJSON format | 1svp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1svp_validation.pdf.gz | 434.3 KB | Display | wwPDB validaton report |
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Full document | 1svp_full_validation.pdf.gz | 438.2 KB | Display | |
Data in XML | 1svp_validation.xml.gz | 15 KB | Display | |
Data in CIF | 1svp_validation.cif.gz | 20.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sv/1svp ftp://data.pdbj.org/pub/pdb/validation_reports/sv/1svp | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.999566, 0.003141, -0.029297), Vector: |
-Components
#1: 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 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56 % | ||||||||||||||||||||||||||||||
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Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Boege, U., (1989) J. Mol. Biol., 208, 79. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 22, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Redundancy: 2.63 % / Rmerge(I) obs: 0.036 |
-Processing
Software |
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Refinement | Resolution: 2→5 Å / σ(F): 0
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Displacement parameters | Biso mean: 29.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→5 Å
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Refine LS restraints |
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