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Yorodumi- PDB-7kvl: SARS-CoV-2 Main protease immature form - FMAX Library E01 fragment -
+Open data
-Basic information
Entry | Database: PDB / ID: 7kvl | ||||||
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Title | SARS-CoV-2 Main protease immature form - FMAX Library E01 fragment | ||||||
Components | 3C-like proteinase | ||||||
Keywords | HYDROLASE / mPro / main protease / COVID-19 / SARS-CoV-2 / 3CL | ||||||
Function / homology | Function and homology information protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs ...protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / TRAF3-dependent IRF activation pathway / Replication of the SARS-CoV-2 genome / snRNP Assembly / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / SARS coronavirus main proteinase / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / symbiont-mediated suppression of host NF-kappaB cascade / 5'-3' DNA helicase activity / host cell endosome / 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 / mRNA (guanine-N7)-methyltransferase / omega peptidase activity / methyltransferase cap1 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / SARS-CoV-2 modulates host translation machinery / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / host cell perinuclear region of cytoplasm / single-stranded RNA binding / host cell endoplasmic reticulum membrane / viral protein processing / lyase activity / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / viral translational frameshifting / RNA-directed RNA polymerase / copper ion binding / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / lipid binding / DNA-templated transcription / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å | ||||||
Authors | Noske, G.D. / Nakamura, A.M. / Gawriljuk, V.O. / Lima, G.M.A. / Zeri, A.C.M. / Nascimento, A.F.Z. / Fernandes, R.S. / Oliva, G. / Godoy, A.S. | ||||||
Funding support | Brazil, 1items
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Citation | Journal: J.Mol.Biol. / Year: 2021 Title: A Crystallographic Snapshot of SARS-CoV-2 Main Protease Maturation Process. Authors: Noske, G.D. / Nakamura, A.M. / Gawriljuk, V.O. / Fernandes, R.S. / Lima, G.M.A. / Rosa, H.V.D. / Pereira, H.D. / Zeri, A.C.M. / Nascimento, A.F.Z. / Freire, M.C.L.C. / Fearon, D. / ...Authors: Noske, G.D. / Nakamura, A.M. / Gawriljuk, V.O. / Fernandes, R.S. / Lima, G.M.A. / Rosa, H.V.D. / Pereira, H.D. / Zeri, A.C.M. / Nascimento, A.F.Z. / Freire, M.C.L.C. / Fearon, D. / Douangamath, A. / von Delft, F. / Oliva, G. / Godoy, A.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7kvl.cif.gz | 262 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kvl.ent.gz | 209.6 KB | Display | PDB format |
PDBx/mmJSON format | 7kvl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kvl_validation.pdf.gz | 767.2 KB | Display | wwPDB validaton report |
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Full document | 7kvl_full_validation.pdf.gz | 773.5 KB | Display | |
Data in XML | 7kvl_validation.xml.gz | 26.4 KB | Display | |
Data in CIF | 7kvl_validation.cif.gz | 37 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kv/7kvl ftp://data.pdbj.org/pub/pdb/validation_reports/kv/7kvl | HTTPS FTP |
-Related structure data
Related structure data | 7kfiSC 7kphC 7kvrC 7ldxC 7lfeC 7lfpC 7mbgC 7n5zC 7n6nC 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 34084.871 Da / Num. of mol.: 2 / Fragment: UNP residues 3264-3569 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: rep, 1a-1b / Production host: Escherichia coli (E. coli) References: UniProt: P0DTD1, SARS coronavirus main proteinase |
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-Non-polymers , 5 types, 239 molecules
#2: Chemical | ChemComp-PEG / #3: Chemical | ChemComp-X4P / | #4: Chemical | ChemComp-DMS / #5: Chemical | ChemComp-SER / | #6: Water | ChemComp-HOH / | |
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-Details
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: 2.58 Å3/Da / Density % sol: 52.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 0.1 M MES, pH 6.7, 5% DMSO, 8% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 1.35502 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 3, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.35502 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.09→72.09 Å / Num. obs: 41380 / % possible obs: 96.8 % / Redundancy: 6.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.07 / Rrim(I) all: 0.176 / Net I/σ(I): 10 / Num. measured all: 261016 / Scaling rejects: 1163 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 7KFI Resolution: 2.09→72.09 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.52 / 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: 126.56 Å2 / Biso mean: 42.8589 Å2 / Biso min: 16.55 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.09→72.09 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Origin x: -2.0074 Å / Origin y: -3.4482 Å / Origin z: 16.6534 Å
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Refinement TLS group |
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