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Yorodumi- PDB-6wks: Structure of SARS-CoV-2 nsp16/nsp10 in complex with RNA cap analo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wks | |||||||||
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Title | Structure of SARS-CoV-2 nsp16/nsp10 in complex with RNA cap analogue (m7GpppA) and S-adenosylmethionine | |||||||||
Components |
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Keywords | RNA BINDING PROTEIN / Enzyme / Transferase / hydrolase / Protein assembly / Methyltransferase | |||||||||
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: 1.8 Å | |||||||||
Authors | Gupta, Y.K. / Viswanathan, T. / Arya, S. / Qi, S. / Misra, A. / Chan, S.-H. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2020 Title: Structural basis of RNA cap modification by SARS-CoV-2. Authors: Viswanathan, T. / Arya, S. / Chan, S.H. / Qi, S. / Dai, N. / Misra, A. / Park, J.G. / Oladunni, F. / Kovalskyy, D. / Hromas, R.A. / Martinez-Sobrido, L. / Gupta, Y.K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wks.cif.gz | 188 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wks.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6wks.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wks_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6wks_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6wks_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 6wks_validation.cif.gz | 29.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/6wks ftp://data.pdbj.org/pub/pdb/validation_reports/wk/6wks | HTTPS FTP |
-Related structure data
Related structure data | 3r24S S: Starting model for refinement |
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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 , 2 types, 2 molecules AAABBB
#1: Protein | Mass: 33355.242 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: rep, 1a-1b / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P0DTD1, Transferases; Transferring one-carbon groups; Methyltransferases |
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#2: Protein | Mass: 14802.930 Da / Num. of mol.: 1 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 BL21(DE3) (bacteria) / References: UniProt: P0DTD1 |
-Non-polymers , 6 types, 256 molecules
#3: Chemical | ChemComp-SAM / | ||||
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#4: Chemical | ChemComp-ADN / | ||||
#5: Chemical | ChemComp-GTA / | ||||
#6: Chemical | #7: Chemical | ChemComp-EDO / | #8: Water | ChemComp-HOH / | |
-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: 4.44 Å3/Da / Density % sol: 72.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 10% (v/v) MPD, 0.1M HEPES pH 7.0 / PH range: 6.0 - 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 18, 2020 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30.002 Å / Num. obs: 78401 / % possible obs: 99.9 % / Redundancy: 20.02 % / Biso Wilson estimate: 34.91 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.042 / Rrim(I) all: 0.13 / Rsym value: 0.13 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.8→1.867 Å / Redundancy: 18.7 % / Rmerge(I) obs: 1.656 / Mean I/σ(I) obs: 1.35 / Num. unique obs: 7772 / CC1/2: 0.707 / CC star: 0.91 / Rpim(I) all: 0.3742 / Rrim(I) all: 1.698 / Rsym value: 1.658 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3r24 Resolution: 1.8→30.002 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.188 / WRfactor Rwork: 0.153 / SU B: 4.226 / SU ML: 0.056 / Average fsc free: 0.9363 / Average fsc work: 0.9446 / Cross valid method: FREE R-VALUE / ESU R: 0.08 / ESU R Free: 0.075 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.686 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→30.002 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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