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Yorodumi- PDB-6zsl: Crystal structure of the SARS-CoV-2 helicase at 1.94 Angstrom res... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zsl | ||||||
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Title | Crystal structure of the SARS-CoV-2 helicase at 1.94 Angstrom resolution | ||||||
Components | SARS-CoV-2 helicase NSP13 | ||||||
Keywords | HYDROLASE / SARS-CoV-2 Helicase NSP13 | ||||||
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: 1.94 Å | ||||||
Authors | Newman, J.A. / Yosaatmadja, Y. / Douangamath, A. / Arrowsmith, C.H. / von Delft, F. / Edwards, A. / Bountra, C. / Gileadi, O. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2021 Title: Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase. Authors: Newman, J.A. / Douangamath, A. / Yadzani, S. / Yosaatmadja, Y. / Aimon, A. / Brandao-Neto, J. / Dunnett, L. / Gorrie-Stone, T. / Skyner, R. / Fearon, D. / Schapira, M. / von Delft, F. / Gileadi, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zsl.cif.gz | 302.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zsl.ent.gz | 194.9 KB | Display | PDB format |
PDBx/mmJSON format | 6zsl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zsl_validation.pdf.gz | 452.3 KB | Display | wwPDB validaton report |
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Full document | 6zsl_full_validation.pdf.gz | 467.2 KB | Display | |
Data in XML | 6zsl_validation.xml.gz | 45 KB | Display | |
Data in CIF | 6zsl_validation.cif.gz | 64.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zs/6zsl ftp://data.pdbj.org/pub/pdb/validation_reports/zs/6zsl | HTTPS FTP |
-Related structure data
Related structure data | 5rl6C 5rl7C 5rl8C 5rl9C 5rlbC 5rlcC 5rldC 5rleC 5rlfC 5rlgC 5rlhC 5rliC 5rljC 5rlkC 5rllC 5rlmC 5rlnC 5rloC 5rlpC 5rlqC 5rlrC 5rlsC 5rltC 5rluC 5rlvC 5rlwC 5rlyC 5rlzC 5rm0C 5rm1C 5rm2C 5rm3C 5rm4C 5rm5C 5rm6C 5rm7C 5rm8C 5rm9C 5rmaC 5rmbC 5rmcC 5rmdC 5rmeC 5rmfC 5rmgC 5rmhC 5rmiC 5rmjC 5rmkC 5rmlC 5rmmC 7nioC 7nn0C 7nngC 6jytS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 67148.805 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: SARS-CoV-2 helicase NSP13 Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: rep, 1a-1b / Production host: Escherichia coli (E. coli) References: UniProt: P0DTD1, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, SARS coronavirus main proteinase, RNA-directed RNA polymerase, DNA ...References: UniProt: P0DTD1, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, SARS coronavirus main proteinase, RNA-directed RNA polymerase, DNA helicase, RNA helicase, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters, Hydrolases; Acting on ester bonds, Transferases; Transferring one-carbon groups; Methyltransferases #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-PO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.3 Å3/Da / Density % sol: 46.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 16 % Ethylene Glycol, 8 % PEG 8000, 0.03M Sodium nitrate, 0.03 Sodium phosphate dibasic, 0.03M Ammonium sulfate, 0.05 M Na HEPES, 0.05 M MOPS |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9126 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9126 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→62.12 Å / Num. obs: 86341 / % possible obs: 97.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 38.29 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.034 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.94→1.97 Å / Rmerge(I) obs: 0.904 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4418 / CC1/2: 0.669 / Rpim(I) all: 0.612 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6JYT Resolution: 1.94→57.56 Å / SU ML: 0.2737 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 32.6506 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 53.58 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.94→57.56 Å
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Refine LS restraints |
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LS refinement shell |
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