+Open data
-Basic information
Entry | Database: PDB / ID: 2snw | |||||||||
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Title | SINDBIS VIRUS CAPSID PROTEIN, TYPE3 CRYSTAL FORM | |||||||||
Components | COAT PROTEIN C | |||||||||
Keywords | VIRAL 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 / 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 / structural molecule activity / virion membrane / proteolysis / RNA binding / membrane Similarity search - Function | |||||||||
Biological species | Sindbis virus | |||||||||
Method | X-RAY DIFFRACTION / MIR, MOLECULAR REPLACEMENT AVERAGING BETWEEN TWO CRYSTAL FORMS / Resolution: 2.7 Å | |||||||||
Authors | Choi, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2snw.cif.gz | 84.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2snw.ent.gz | 64.4 KB | Display | PDB format |
PDBx/mmJSON format | 2snw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2snw_validation.pdf.gz | 424.2 KB | Display | wwPDB validaton report |
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Full document | 2snw_full_validation.pdf.gz | 429.1 KB | Display | |
Data in XML | 2snw_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 2snw_validation.cif.gz | 17.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sn/2snw ftp://data.pdbj.org/pub/pdb/validation_reports/sn/2snw | HTTPS FTP |
-Related structure data
Related structure data | 1kxaC 1kxbC 1kxcC 1kxdC 1kxeC 1kxfC C: citing same article (ref.) |
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Similar structure data |
-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: (0.805227, 0.436695, 0.401132), Vector: |
-Components
#1: 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 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54 % / Description: THESE ARE RE-REFINED COORDINATES OF 1SNW. | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 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
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-Data collection
Diffraction | Mean temperature: 285 K |
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Diffraction source | Source: ROTATING ANODE / Type: ELLIOTT GX-20 / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Feb 1, 1992 / Details: BENT FOCUSING MIRROR |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 % |
-Processing
Software |
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Refinement | Method 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
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Displacement parameters | Biso mean: 33.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 30 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→8 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: MOL1 AND MOL4, MOL2 AND MOL3 WERE RESTRAINED IN A PAIRWISE MANNER DURING REFINEMENT. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.76 Å / Total num. of bins used: 14
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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