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Yorodumi- PDB-7ldx: SARS-CoV-2 Main protease immature form - F2X Entry Library E06 fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ldx | |||||||||
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Title | SARS-CoV-2 Main protease immature form - F2X Entry Library E06 fragment | |||||||||
Components | 3C-like proteinase | |||||||||
Keywords | HYDROLASE / 3cl / protease / sars / sars-cov-2 / covid / main protease | |||||||||
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 / 5'-3' DNA helicase activity / SARS coronavirus main proteinase / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 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 / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / 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 / single-stranded RNA binding / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / copper ion binding / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / DNA-templated transcription / lipid binding / 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: 2.23 Å | |||||||||
Authors | Noske, G.D. / Nakamura, A.M. / Gawriljuk, V.O. / Lima, G.M.A. / Zeri, A.C.M. / Nascimento, A.F.Z. / 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 | 7ldx.cif.gz | 250.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ldx.ent.gz | 199.5 KB | Display | PDB format |
PDBx/mmJSON format | 7ldx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ldx_validation.pdf.gz | 1019 KB | Display | wwPDB validaton report |
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Full document | 7ldx_full_validation.pdf.gz | 1014.7 KB | Display | |
Data in XML | 7ldx_validation.xml.gz | 24.8 KB | Display | |
Data in CIF | 7ldx_validation.cif.gz | 34.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ld/7ldx ftp://data.pdbj.org/pub/pdb/validation_reports/ld/7ldx | HTTPS FTP |
-Related structure data
Related structure data | 7kfiSC 7kphC 7kvlC 7kvrC 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
#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 #2: Chemical | #3: Chemical | ChemComp-DMS / #4: Chemical | #5: 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: 2.62 Å3/Da / Density % sol: 53.03 % |
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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 | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.35502 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.23→56.21 Å / Num. obs: 21562 / % possible obs: 61.5 % / Redundancy: 1.9 % / CC1/2: 0.649 / Rmerge(I) obs: 0.318 / Rpim(I) all: 0.318 / Rrim(I) all: 0.449 / Net I/σ(I): 5.1 / Num. measured all: 40531 | ||||||||||||||||||||||||||||||
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: 2.23→56.21 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.23 / 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: 111.66 Å2 / Biso mean: 29.1637 Å2 / Biso min: 6.27 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.23→56.21 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: -1.8918 Å / Origin y: -3.4803 Å / Origin z: 16.4708 Å
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Refinement TLS group |
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