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Yorodumi- PDB-6vh2: 2.26 A resolution structure of MERS 3CL protease in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vh2 | |||||||||
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Title | 2.26 A resolution structure of MERS 3CL protease in complex with inhibitor 7i | |||||||||
Components | Orf1a proteinORF1ab | |||||||||
Keywords | Hydrolase/Hydrolase Inhibitor / PROTEASE / MERS 3CL protease Inhhibitors / HYDROLASE / Hydrolase-Hydrolase Inhibitor complex | |||||||||
Function / homology | Function and homology information host cell membrane / endoplasmic reticulum-Golgi intermediate compartment / viral genome replication / methyltransferase activity / methylation / 3'-5'-RNA exonuclease activity / : / host cell endoplasmic reticulum-Golgi intermediate compartment / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation ...host cell membrane / endoplasmic reticulum-Golgi intermediate compartment / viral genome replication / methyltransferase activity / methylation / 3'-5'-RNA exonuclease activity / : / host cell endoplasmic reticulum-Golgi intermediate compartment / 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 / mRNA (nucleoside-2'-O-)-methyltransferase activity / endonuclease activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / cysteine-type deubiquitinase activity / RNA helicase activity / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / induction by virus of host autophagy / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / proteolysis / zinc ion binding / ATP binding / membrane Similarity search - Function | |||||||||
Biological species | Middle East respiratory syndrome-related coronavirus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.26 Å | |||||||||
Authors | Lovell, S. / Battaile, K.P. / Kashipathy, M.M. / Rathnayake, A.D. / Zheng, J. / Kim, Y. / Nguyen, H.N. / Chang, K.O. / Groutas, W.C. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Sci Transl Med / Year: 2020 Title: 3C-like protease inhibitors block coronavirus replication in vitro and improve survival in MERS-CoV-infected mice. Authors: Rathnayake, A.D. / Zheng, J. / Kim, Y. / Perera, K.D. / Mackin, S. / Meyerholz, D.K. / Kashipathy, M.M. / Battaile, K.P. / Lovell, S. / Perlman, S. / Groutas, W.C. / Chang, K.O. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vh2.cif.gz | 132 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vh2.ent.gz | 99.3 KB | Display | PDB format |
PDBx/mmJSON format | 6vh2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vh/6vh2 ftp://data.pdbj.org/pub/pdb/validation_reports/vh/6vh2 | HTTPS FTP |
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-Related structure data
Related structure data | 6vgyC 6vgzC 6vh0C 6vh1C 6vh3C 6w2aC 6xmkC 5wkkS 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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Unit cell |
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-Components
#1: Protein | Mass: 34314.242 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: N-terminal hexahistidine tag Source: (gene. exp.) Middle East respiratory syndrome-related coronavirus Gene: orf1a / Plasmid: pET28 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A1L2E0X0, UniProt: T2B9U0*PLUS #2: Chemical | #3: 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: 2.54 Å3/Da / Density % sol: 51.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 15% (w/v) PEG 4000, 100 mM sodium citrate, 100 mM magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 3, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.256→45.55 Å / Num. obs: 33514 / % possible obs: 99.6 % / Redundancy: 6.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.128 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.256→2.33 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.918 / Num. unique obs: 3006 / CC1/2: 0.752 / % possible all: 98.8 |
-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5WKK Resolution: 2.26→39.07 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.31 / Phase error: 25.73 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 87.57 Å2 / Biso mean: 38.9359 Å2 / Biso min: 19.51 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.26→39.07 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11
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