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Open data
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Basic information
Entry | Database: PDB / ID: 1vcp | ||||||
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Title | SEMLIKI FOREST VIRUS CAPSID PROTEIN (CRYSTAL FORM I) | ||||||
![]() | SEMLIKI FOREST VIRUS CAPSID PROTEIN | ||||||
![]() | VIRAL PROTEIN / VIRUS COAT PROTEIN / POLYPROTEIN / TRANSMEMBRANE / GLYCOPROTEIN / NUCLEOCAPSID PROTEIN | ||||||
Function / homology | ![]() 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 / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope ...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 / 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 | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Lu, G. / Choi, H.-K. / Rossmann, M.G. | ||||||
![]() | ![]() Title: Structure of Semliki Forest virus core protein. Authors: Choi, H.K. / Lu, G. / Lee, S. / Wengler, G. / Rossmann, M.G. #1: ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 95.3 KB | Display | ![]() |
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PDB format | ![]() | 73.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 426.9 KB | Display | ![]() |
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Full document | ![]() | 439 KB | Display | |
Data in XML | ![]() | 18.4 KB | Display | |
Data in CIF | ![]() | 24.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 16252.439 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: CRYSTAL FORM 1 / Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.85 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | 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 ...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
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: SIEMENS / Detector: AREA DETECTOR |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. 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
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Refinement | Resolution: 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.
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Displacement parameters | Biso mean: 12.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→6 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |