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- PDB-7nn0: Crystal structure of the SARS-CoV-2 helicase in complex with AMP-PNP -
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Open data
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Basic information
Entry | Database: PDB / ID: 7nn0 | ||||||
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Title | Crystal structure of the SARS-CoV-2 helicase in complex with AMP-PNP | ||||||
![]() | SARS-CoV-2 helicase NSP13 | ||||||
![]() | HYDROLASE / NSP13 / Helicase / SARS-CoV-2 | ||||||
Function / homology | ![]() 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 / 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 / SARS-CoV-2 modulates host translation machinery / 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 / mRNA (nucleoside-2'-O-)-methyltransferase activity / DNA helicase / 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 endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / 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 / 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 / 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Newman, J.A. / Yosaatmadja, Y. / Douangamath, A. / Bountra, C. / Gileadi, O. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 456.7 KB | Display | ![]() |
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PDB format | ![]() | 369.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 81.2 KB | Display | |
Data in CIF | ![]() | 107.5 KB | Display | |
Arichive directory | ![]() ![]() | 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 ![]() 6zslSC ![]() 7nioC ![]() 7nngC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 67148.805 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: rep, 1a-1b / Production host: ![]() ![]() 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-ANP / #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20 % Ethylene Glycol, 10 % PEG 8K, 0.05 M MES pH 6.5, 0.05 M Imidazole pH 6.5, 10% v/v Alcohols mix |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 22, 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: 3.04→81.03 Å / Num. obs: 48372 / % possible obs: 97.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 60.23 Å2 / CC1/2: 0.978 / Rmerge(I) obs: 0.258 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 3.04→3.09 Å / Rmerge(I) obs: 1.39 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2343 / CC1/2: 0.359 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6ZSL Resolution: 3.04→81.03 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.08 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.04→81.03 Å
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Refine LS restraints |
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LS refinement shell |
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