[English] 日本語
Yorodumi- PDB-6vh3: 2.20 A resolution structure of MERS 3CL protease in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vh3 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | 2.20 A resolution structure of MERS 3CL protease in complex with inhibitor 7j | |||||||||
Components | Orf1a protein | |||||||||
Keywords | HYDROLASE/HYDROLASE Inhibitor / PROTEASE / MERS 3CL protease Inhhibitors / HYDROLASE / HYDROLASE-HYDROLASE Inhibitor complex | |||||||||
Function / homology | Function and homology information host cell membrane / viral genome replication / methyltransferase activity / 5'-3' DNA helicase activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity ...host cell membrane / viral genome replication / methyltransferase activity / 5'-3' DNA helicase activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / 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 / methylation / endonuclease activity / mRNA (nucleoside-2'-O-)-methyltransferase 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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / proteolysis / zinc ion binding / ATP binding / membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Middle East respiratory syndrome-related coronavirus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 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
| |||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6vh3.cif.gz | 131.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6vh3.ent.gz | 98.9 KB | Display | PDB format |
PDBx/mmJSON format | 6vh3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vh/6vh3 ftp://data.pdbj.org/pub/pdb/validation_reports/vh/6vh3 | HTTPS FTP |
---|
-Related structure data
Related structure data | 6vgyC 6vgzC 6vh0C 6vh1C 6vh2C 6w2aC 6xmkC 5wkkS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.93 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 25% (w/v) PEG 3350, 100 mM Bis-Tris, 200 mM ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→45.48 Å / Num. obs: 35788 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.141 / Net I/σ(I): 9.3 / Num. measured all: 238120 |
Reflection shell | Resolution: 2.2→2.27 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.04 / Num. measured all: 20362 / Num. unique obs: 3067 / CC1/2: 0.74 / Net I/σ(I) obs: 1.9 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Model details: Phaser MODE: MR_AUTO
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5WKK Resolution: 2.2→43.827 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.13 / Phase error: 24.74 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 114.81 Å2 / Biso mean: 37.9009 Å2 / Biso min: 18.11 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→43.827 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
|