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Yorodumi- PDB-4wmd: Crystal structure of catalytically inactive MERS-CoV 3CL protease... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wmd | ||||||
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Title | Crystal structure of catalytically inactive MERS-CoV 3CL protease (C148A) in spacegroup C2221 | ||||||
Components | ORF1aORF1ab | ||||||
Keywords | HYDROLASE / 3CL protease / MERS / coronavirus | ||||||
Function / homology | Function and homology information host cell membrane / viral genome replication / methyltransferase activity / methylation / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / cysteine-type deubiquitinase activity ...host cell membrane / viral genome replication / methyltransferase activity / methylation / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / cysteine-type deubiquitinase activity / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / virus-mediated perturbation of host defense response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / cysteine-type endopeptidase activity / proteolysis / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Middle East respiratory syndrome coronavirus | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.585 Å | ||||||
Authors | Lountos, G.T. / Needle, D. / Waugh, D.S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: Structures of the Middle East respiratory syndrome coronavirus 3C-like protease reveal insights into substrate specificity. Authors: Needle, D. / Lountos, G.T. / Waugh, D.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wmd.cif.gz | 188.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wmd.ent.gz | 150.5 KB | Display | PDB format |
PDBx/mmJSON format | 4wmd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/4wmd ftp://data.pdbj.org/pub/pdb/validation_reports/wm/4wmd | HTTPS FTP |
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-Related structure data
Related structure data | 4wmeC 4wmfC 2ynaS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 33322.109 Da / Num. of mol.: 3 / Mutation: C148A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Middle East respiratory syndrome coronavirus Plasmid: pDN2551 / Production host: Escherichia coli (E. coli) / References: UniProt: W6A941 |
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-Non-polymers , 5 types, 291 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PG4 / | #5: Chemical | ChemComp-1PE / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.28 Å3/Da / Density % sol: 71.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20.3 mg/mL protein, well solution: 0.1M Tris-Bis Tris pH 8.5, 0.12M ethylene glycols, 30% (v/v) ethylene glycol-polyethylene glycol 8000, (Morpheus Screeen condition E10). PH range: 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 1, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.58→50 Å / Num. obs: 53763 / % possible obs: 99.9 % / Redundancy: 7.5 % / Rsym value: 0.077 / Net I/σ(I): 23.5 |
Reflection shell | Resolution: 2.58→2.62 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.646 / Mean I/σ(I) obs: 2 / % possible all: 99.7 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: dev_1448) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2YNA chain A Resolution: 2.585→46.162 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 39.84 / Phase error: 23.01 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.585→46.162 Å
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Refine LS restraints |
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LS refinement shell |
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