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Yorodumi- PDB-6wjt: 2.0 Angstrom Resolution Crystal Structure of Nsp16-Nsp10 Heterodi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wjt | ||||||
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Title | 2.0 Angstrom Resolution Crystal Structure of Nsp16-Nsp10 Heterodimer from SARS-CoV-2 in Complex with S-Adenosyl-L-Homocysteine | ||||||
Components |
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Keywords | VIRAL PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / nsp16 / nsp10 / complex / S-Adenosyl-L-Homocysteine | ||||||
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 Å | ||||||
Authors | Minasov, G. / Shuvalova, L. / Rosas-Lemus, M. / Kiryukhina, O. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: Sci.Signal. / Year: 2020 Title: High-resolution structures of the SARS-CoV-2 2'- O -methyltransferase reveal strategies for structure-based inhibitor design. Authors: Rosas-Lemus, M. / Minasov, G. / Shuvalova, L. / Inniss, N.L. / Kiryukhina, O. / Brunzelle, J. / Satchell, K.J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wjt.cif.gz | 345.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wjt.ent.gz | 279.3 KB | Display | PDB format |
PDBx/mmJSON format | 6wjt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wjt_validation.pdf.gz | 3.2 MB | Display | wwPDB validaton report |
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Full document | 6wjt_full_validation.pdf.gz | 3.2 MB | Display | |
Data in XML | 6wjt_validation.xml.gz | 38.5 KB | Display | |
Data in CIF | 6wjt_validation.cif.gz | 56.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wj/6wjt ftp://data.pdbj.org/pub/pdb/validation_reports/wj/6wjt | HTTPS FTP |
-Related structure data
Related structure data | 6w4hC 6w75SC 6wkqC 6wq3C 6wrzC 6wvnC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 33627.504 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: rep, 1a-1b / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): magic References: UniProt: P0DTD1, Transferases; Transferring one-carbon groups; Methyltransferases #2: Protein | Mass: 15075.190 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: rep, 1a-1b / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): magic / References: UniProt: P0DTD1 |
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-Non-polymers , 5 types, 594 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-FMT / #6: Chemical | ChemComp-ZN / #7: 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: 3.98 Å3/Da / Density % sol: 69.08 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Protein: 5.3 mg/ml (nsp10/nsp16 1:1), 0.15M Sodium chloride, 0.01M Tris pH 7.5 , 2mM SAM, 1mM TCEP, 5% Glycerol; Screen: ComPAS (F10), 0.4M Potassium/Sodium tartrate; Soak and Cryo: 5mM SAH, ...Details: Protein: 5.3 mg/ml (nsp10/nsp16 1:1), 0.15M Sodium chloride, 0.01M Tris pH 7.5 , 2mM SAM, 1mM TCEP, 5% Glycerol; Screen: ComPAS (F10), 0.4M Potassium/Sodium tartrate; Soak and Cryo: 5mM SAH, 4M Sodium formate, 3 hrs. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 3, 2020 / Details: Be |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 105884 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 34.2 Å2 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.044 / Rrim(I) all: 0.11 / Rsym value: 0.101 / Χ2: 1.003 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 5270 / CC1/2: 0.933 / CC star: 0.982 / Rpim(I) all: 0.34 / Rrim(I) all: 0.866 / Rsym value: 0.795 / Χ2: 1.003 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6w75 Resolution: 2→29.79 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.627 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.105 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 140.57 Å2 / Biso mean: 40.744 Å2 / Biso min: 21.59 Å2
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Refinement step | Cycle: final / Resolution: 2→29.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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