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Yorodumi- PDB-7jib: Room Temperature Crystal Structure of Nsp10/Nsp16 from SARS-CoV-2... -
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-Basic information
Entry | Database: PDB / ID: 7jib | ||||||
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Title | Room Temperature Crystal Structure of Nsp10/Nsp16 from SARS-CoV-2 with Substrates and Products of 2'-O-methylation of the Cap-1 | ||||||
Components |
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Keywords | VIRAL PROTEIN / SARS CoV-2 / Methyltransferase / m7GpppA / Cap-0 / Cap-1 / SAH / SAM / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
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 / 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 | Severe acute respiratory syndrome coronavirus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Wilamowski, M. / Minasov, G. / Kim, Y. / Sherrell, D.A. / Shuvalova, L. / Lavens, A. / Chard, R. / Rosas-Lemus, M. / Maltseva, N. / Jedrzejczak, R. ...Wilamowski, M. / Minasov, G. / Kim, Y. / Sherrell, D.A. / Shuvalova, L. / Lavens, A. / Chard, R. / Rosas-Lemus, M. / Maltseva, N. / Jedrzejczak, R. / Michalska, K. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2021 Title: 2'-O methylation of RNA cap in SARS-CoV-2 captured by serial crystallography. Authors: Wilamowski, M. / Sherrell, D.A. / Minasov, G. / Kim, Y. / Shuvalova, L. / Lavens, A. / Chard, R. / Maltseva, N. / Jedrzejczak, R. / Rosas-Lemus, M. / Saint, N. / Foster, I.T. / Michalska, K. ...Authors: Wilamowski, M. / Sherrell, D.A. / Minasov, G. / Kim, Y. / Shuvalova, L. / Lavens, A. / Chard, R. / Maltseva, N. / Jedrzejczak, R. / Rosas-Lemus, M. / Saint, N. / Foster, I.T. / Michalska, K. / Satchell, K.J.F. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jib.cif.gz | 195.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jib.ent.gz | 151.5 KB | Display | PDB format |
PDBx/mmJSON format | 7jib.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jib_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 7jib_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 7jib_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | 7jib_validation.cif.gz | 26.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ji/7jib ftp://data.pdbj.org/pub/pdb/validation_reports/ji/7jib | HTTPS FTP |
-Related structure data
Related structure data | 6xkmC 7jheC 7jpeC 6wq3S C: citing same article (ref.) 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 AB
#1: Protein | Mass: 33627.504 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: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Magic References: UniProt: P0DTD1, Transferases; Transferring one-carbon groups; Methyltransferases |
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#2: Protein | Mass: 15075.190 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) / Strain (production host): BL21(DE3) / Variant (production host): Magic / References: UniProt: P0DTD1 |
-Non-polymers , 8 types, 150 molecules
#3: Chemical | #4: Chemical | ChemComp-SAM / | #5: Chemical | ChemComp-SAH / | #6: Chemical | ChemComp-GTA / | #7: Chemical | ChemComp-V9G / | #8: Chemical | ChemComp-MGP / | #9: Chemical | #10: 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: 4.49 Å3/Da / Density % sol: 72.6 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Protein: 4.0 mg/ml (Nsp10/Nsp16 1:1), 0.15 M NaCl, 0.01 M Tris-HCl, 2 mM SAM, 1 mM TCEP, 5% Glycerol, pH 7.5. Precipitation buffer: 0.1 M MES pH 6.5, 0.9 M NaF. Sitting drops made using 0.4 ...Details: Protein: 4.0 mg/ml (Nsp10/Nsp16 1:1), 0.15 M NaCl, 0.01 M Tris-HCl, 2 mM SAM, 1 mM TCEP, 5% Glycerol, pH 7.5. Precipitation buffer: 0.1 M MES pH 6.5, 0.9 M NaF. Sitting drops made using 0.4 ul of protein mixed with 0.4 ul of precipitation buffer. |
-Data collection
Diffraction | Mean temperature: 295 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jul 10, 2020 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→50 Å / Num. obs: 25799 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 49.9 Å2 / CC1/2: 0.981 / CC star: 0.995 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.071 / Χ2: 1.248 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.65→2.7 Å / Redundancy: 4.9 % / Rmerge(I) obs: 1.037 / Mean I/σ(I) obs: 1.87 / Num. unique obs: 1263 / CC1/2: 0.537 / CC star: 0.836 / Rpim(I) all: 0.507 / Χ2: 1.007 / % possible all: 99.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6WQ3 Resolution: 2.65→29.59 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 16.148 / SU ML: 0.159 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.25 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 186.47 Å2 / Biso mean: 55.906 Å2 / Biso min: 13.6 Å2
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Refinement step | Cycle: final / Resolution: 2.65→29.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.718 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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