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Yorodumi- PDB-8e7t: Crystal structure of Middle East respiratory syndrome coronavirus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8e7t | ||||||
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Title | Crystal structure of Middle East respiratory syndrome coronavirus (MERS-CoV) 3CL protease inactive mutant C148A | ||||||
Components | 3C-Like Protease | ||||||
Keywords | VIRAL PROTEIN / MERS / Coronavirus / PROTEASE / DRUG RESISTANCE / HYDROLASE / DURG DISCOVERY / 3CL protease / inactive / inactive mutant | ||||||
Function / homology | Function and homology information host cell membrane / viral genome replication / methyltransferase activity / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / methylation / symbiont-mediated perturbation of host ubiquitin-like protein modification / cysteine-type deubiquitinase activity ...host cell membrane / viral genome replication / methyltransferase activity / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / methylation / 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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / cysteine-type endopeptidase activity / virus-mediated perturbation of host defense response / proteolysis / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Middle East respiratory syndrome-related coronavirus | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Shaqra, A.M. / Zvornicanin, S.N. / Schiffer, C.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal structure of Middle East respiratory syndrome coronavirus (MERS-CoV) 3CL protease inactive mutant C148A Authors: Shaqra, A.M. / Zvornicanin, S.N. / Schiffer, C.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8e7t.cif.gz | 258.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8e7t.ent.gz | 205.1 KB | Display | PDB format |
PDBx/mmJSON format | 8e7t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8e7t_validation.pdf.gz | 3.2 MB | Display | wwPDB validaton report |
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Full document | 8e7t_full_validation.pdf.gz | 3.2 MB | Display | |
Data in XML | 8e7t_validation.xml.gz | 50.4 KB | Display | |
Data in CIF | 8e7t_validation.cif.gz | 71 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e7/8e7t ftp://data.pdbj.org/pub/pdb/validation_reports/e7/8e7t | HTTPS FTP |
-Related structure data
Related structure data | 4wmeS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 33322.109 Da / Num. of mol.: 4 / Mutation: C148A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Middle East respiratory syndrome-related coronavirus Production host: Escherichia coli (E. coli) / References: UniProt: W6A941 #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-NA / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.52 Å3/Da / Density % sol: 51.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 10-20 % (w/v) PEG3350, 0.20-0.30 M NaCl, and 0.1 M Bis-Tris methane pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: May 4, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→24.93 Å / Num. obs: 45868 / % possible obs: 99.86 % / Redundancy: 7.3 % / Biso Wilson estimate: 29 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.1909 / Rpim(I) all: 0.07489 / Rrim(I) all: 0.2055 / Net I/σ(I): 10.61 |
Reflection shell | Resolution: 2.5→2.589 Å / Redundancy: 7.4 % / Num. unique obs: 4543 / CC1/2: 0.675 / CC star: 0.898 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WME Resolution: 2.5→24.93 Å / SU ML: 0.3152 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.7895 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.83 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→24.93 Å
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Refine LS restraints |
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LS refinement shell |
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