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Yorodumi- PDB-2wv5: Crystal structure of foot-and-mouth disease virus 3C protease in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wv5 | ||||||
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Title | Crystal structure of foot-and-mouth disease virus 3C protease in complex with a decameric peptide corresponding to the VP1-2A cleavage junction with a GLN to Glu substitution at P1 | ||||||
Components |
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Keywords | HYDROLASE/PEPTIDE / 3C PROTEASE / HYDROLASE / VIRAL PROTEIN / HYDROLASE PEPTIDE COMPLEX / HYDROLASE-PEPTIDE complex | ||||||
Function / homology | Function and homology information L-peptidase / modulation by virus of host chromatin organization / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / viral capsid / : / nucleoside-triphosphate phosphatase / regulation of translation ...L-peptidase / modulation by virus of host chromatin organization / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / viral capsid / : / nucleoside-triphosphate phosphatase / regulation of translation / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / induction by virus of host autophagy / symbiont entry into host cell / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | FOOT-AND-MOUTH DISEASE VIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Zunszain, P.A. / Knox, S.R. / Sweeney, T.R. / Yang, J. / Roque-Rosell, N. / Belsham, G.J. / Leatherbarrow, R.J. / Curry, S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Insights Into Cleavage Specificity from the Crystal Structure of Foot-and-Mouth Disease Virus 3C Protease Complexed with a Peptide Substrate. Authors: Zunszain, P.A. / Knox, S.R. / Sweeney, T.R. / Yang, J. / Roque-Rosell, N. / Belsham, G.J. / Leatherbarrow, R.J. / Curry, S. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -4-STRANDED BARREL THIS IS REPRESENTED BY A -3-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -2-STRANDED BARREL THIS IS REPRESENTED BY A -1-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wv5.cif.gz | 162.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wv5.ent.gz | 127.4 KB | Display | PDB format |
PDBx/mmJSON format | 2wv5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/2wv5 ftp://data.pdbj.org/pub/pdb/validation_reports/wv/2wv5 | HTTPS FTP |
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-Related structure data
Related structure data | 2wv4C 2j92S S: Starting model for refinement 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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2 |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 23049.654 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) FOOT-AND-MOUTH DISEASE VIRUS / Strain: A10-61 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03306, picornain 3C #2: Protein/peptide | Mass: 1144.297 Da / Num. of mol.: 4 / Fragment: VP1-2A CLEAVAGE JUNCTION (P5-P5'), RESIDUES 29-38 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) FOOT-AND-MOUTH DISEASE VIRUS / References: UniProt: Q65050, UniProt: P03306*PLUS #3: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, CYS1744 TO LYS ENGINEERED RESIDUE IN CHAIN A, CYS1791 TO LEU ...ENGINEERED | Sequence details | CONTAINS ADDITIONAL GLY AS RESIDUE 1. LAST 6 RESIDUES AT C- TERM MISSING FROM OUR STRUCTURE. ...CONTAINS ADDITIONAL | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45 % / Description: NONE |
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Crystal grow | pH: 8 / Details: SEE PAPER, pH 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 15, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→63.2 Å / Num. obs: 16981 / % possible obs: 76.1 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 45.5 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.2 / % possible all: 60.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2J92 Resolution: 2.7→56.33 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 666675.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.132 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→56.33 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
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Xplor file |
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