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- PDB-2q6g: Crystal structure of SARS-CoV main protease H41A mutant in comple... -
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Basic information
Entry | Database: PDB / ID: 2q6g | ||||||
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Title | Crystal structure of SARS-CoV main protease H41A mutant in complex with an N-terminal substrate | ||||||
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![]() | HYDROLASE / coronavirus / SARS-CoV / main protease / 3C-Like proteinase / substrate | ||||||
Function / homology | ![]() viral RNA-directed RNA polymerase complex / exoribonuclease complex / viral replication complex formation and maintenance / : / cytoplasmic viral factory / positive regulation of ubiquitin-specific protease activity / symbiont-mediated suppression of host translation / symbiont-mediated suppression of host TRAF-mediated signal transduction => GO:0039527 / endopeptidase complex / endoribonuclease complex ...viral RNA-directed RNA polymerase complex / exoribonuclease complex / viral replication complex formation and maintenance / : / cytoplasmic viral factory / positive regulation of ubiquitin-specific protease activity / symbiont-mediated suppression of host translation / symbiont-mediated suppression of host TRAF-mediated signal transduction => GO:0039527 / endopeptidase complex / endoribonuclease complex / : / mRNA capping enzyme complex / suppression by virus of host type I interferon production / positive stranded viral RNA replication / positive regulation of RNA biosynthetic process / protein K48-linked deubiquitination / : / : / Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / protein K63-linked deubiquitination / Translation of Replicase and Assembly of the Replication Transcription Complex / K48-linked deubiquitinase activity / Replication of the SARS-CoV-1 genome / host cell endoplasmic reticulum / K63-linked deubiquitinase activity / RNA-templated transcription / SARS-CoV-1 modulates host translation machinery / viral transcription / protein autoprocessing / 7-methylguanosine mRNA capping / positive regulation of viral genome replication / DNA helicase activity / Transferases; Transferring one-carbon groups; Methyltransferases / helicase activity / protein processing / SARS-CoV-1 activates/modulates innate immune responses / double-stranded RNA binding / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / ISG15-specific peptidase activity / symbiont-mediated suppression of host gene expression / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 5'-3' DNA helicase activity / SARS coronavirus main proteinase / host cell endosome / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / DNA helicase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / host cell cytoplasm / cysteine-type deubiquitinase activity / membrane => GO:0016020 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / protein dimerization activity / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Xue, X.Y. / Yang, H.T. / Xue, F. / Bartlam, M. / Rao, Z.H. | ||||||
![]() | ![]() Title: Structures of two coronavirus main proteases: implications for substrate binding and antiviral drug design. Authors: Xue, X. / Yu, H. / Yang, H. / Xue, F. / Wu, Z. / Shen, W. / Li, J. / Zhou, Z. / Ding, Y. / Zhao, Q. / Zhang, X.C. / Liao, M. / Bartlam, M. / Rao, Z. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 134.5 KB | Display | ![]() |
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PDB format | ![]() | 105.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 451.7 KB | Display | ![]() |
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Full document | ![]() | 469.7 KB | Display | |
Data in XML | ![]() | 28.1 KB | Display | |
Data in CIF | ![]() | 39.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2q6dC ![]() 2q6fC ![]() 1uk2S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | The biological assembly is a homodimer with two substrate molecule in the active site of each protomer. |
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Components
#1: Protein | Mass: 33809.566 Da / Num. of mol.: 2 / Mutation: H41A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P59641, UniProt: P0C6X7*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases #2: Protein/peptide | Mass: 1195.369 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized. / References: UniProt: P0C6X7*PLUS #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.6 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 2% polyethylene glycol (PEG) 6000 3% DMSO 1 mM DTT 0.1 M [2-(N-morpholino) ethanesulfonic acid] (Mes) buffer (pH 6.0). The 11-mer peptidyl substrate with sequence TSAVLQSGFRK was dissolved ...Details: 2% polyethylene glycol (PEG) 6000 3% DMSO 1 mM DTT 0.1 M [2-(N-morpholino) ethanesulfonic acid] (Mes) buffer (pH 6.0). The 11-mer peptidyl substrate with sequence TSAVLQSGFRK was dissolved in 7.5% PEG 6000, 6% DMSO, and 0.1MMes (pH 6.0) with a concentration of 20 mM. A 3 l aliquot of such solution was added to the drop and the crystals were soaked for 8 days., VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 18, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 82777 / Num. obs: 25190 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.106 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2512 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1UK2 Resolution: 2.5→30 Å / Isotropic thermal model: Isotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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