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Yorodumi- PDB-7koa: Room Temperature Structure of SARS-CoV-2 Nsp10/16 Methyltransfera... -
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-Basic information
Entry | Database: PDB / ID: 7koa | ||||||
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Title | Room Temperature Structure of SARS-CoV-2 Nsp10/16 Methyltransferase in a Complex with Cap-0 and SAM Determined by Pink-Beam Serial Crystallography | ||||||
Components |
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Keywords | VIRAL PROTEIN / SARS CoV-2 / Serial Crystallography / Methyltransferase / m7GpppA / Cap-0 / S-adenosylhomometionine / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Lyases; Phosphorus-oxygen lyases / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Lyases; Phosphorus-oxygen lyases / 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 / snRNP Assembly / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / SARS coronavirus main proteinase / host cell endosome / 3'-5'-RNA exonuclease activity / : / host cell endoplasmic reticulum-Golgi intermediate compartment / 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 / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / DNA helicase / 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 / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / copper ion binding / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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: 2.4 Å | ||||||
Authors | Wilamowski, M. / Sherrell, D.A. / Minasov, G. / Shuvalova, L. / Lavens, A. / Henning, R. / Maltseva, N. / Rosas-Lemus, M. / Kim, Y. / Satchell, K.J.F. ...Wilamowski, M. / Sherrell, D.A. / Minasov, G. / Shuvalova, L. / Lavens, A. / Henning, R. / Maltseva, N. / Rosas-Lemus, M. / Kim, Y. / Satchell, K.J.F. / Srajer, V. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To Be Published Title: Room Temperature Structure of SARS-CoV-2 Nsp10/Nsp16 Methyltransferase in a Complex with Cap-0 and SAM Determined by Pink-Beam Serial Crystallography Authors: Wilamowski, M. / Sherrell, D.A. / Minasov, G. / Shuvalova, L. / Lavens, A. / Henning, R. / Maltseva, N. / Rosas-Lemus, M. / Kim, Y. / Satchell, K.J.F. / Srajer, V. / Joachimiak, A. / Center ...Authors: Wilamowski, M. / Sherrell, D.A. / Minasov, G. / Shuvalova, L. / Lavens, A. / Henning, R. / Maltseva, N. / Rosas-Lemus, M. / Kim, Y. / Satchell, K.J.F. / Srajer, V. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7koa.cif.gz | 107.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7koa.ent.gz | 79.1 KB | Display | PDB format |
PDBx/mmJSON format | 7koa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ko/7koa ftp://data.pdbj.org/pub/pdb/validation_reports/ko/7koa | HTTPS FTP |
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-Related structure data
Related structure data | 6xkmS 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 , 4 types, 187 molecules
#3: Chemical | #4: Chemical | ChemComp-SAM / | #5: Chemical | #6: 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: 1817 |
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-Sample preparation
Crystal | Density Matthews: 4.46 Å3/Da / Density % sol: 72.5 % |
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Crystal grow | Temperature: 298 K / Method: batch mode / 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. Batch crystallization: 100 ...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. Batch crystallization: 100 ul of protein mixed with 100 ul of precipitation buffer in 500 ul polypropylane tube. Crystals were soaked with m7GpppA (0.5 mM) for 10 minutes before data collection. |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: Y | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.02-1.18 | |||||||||
Detector | Type: RAYONIX MX340-HS / Detector: CCD / Date: Sep 18, 2020 | |||||||||
Radiation | Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.4→49.7 Å / Num. obs: 22795 / % possible obs: 65.85 % / Redundancy: 7.4 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.129 / Net I/σ(I): 16.5 | |||||||||
Reflection shell | Resolution: 2.4→2.51 Å / Rmerge(I) obs: 0.105 / Num. unique obs: 669 / % possible all: 15.63 | |||||||||
Serial crystallography sample delivery | Description: Nylon Mesh / Method: fixed target | |||||||||
Serial crystallography sample delivery fixed target | Crystals per unit: 1 / Description: ALEX mesh holder / Details: start/stop raster over area / Motion control: SmarAct Motors viaPMAC / Sample dehydration prevention: 6 um Mylar sandwich / Sample holding: nylon mesh Sample solvent: 50 mM MES pH 6.5, 0.45 M NaF, 75 mM NaCl, 5 mM Tris-HCl, 1 mM SAM, 0.5 mM TCEP, 2.5 % glycerol, 0.5 mM m7GpppA Sample unit size: 90 µm / Support base: xyz stage / Velocity horizontal: 10 / Velocity vertical: 10 | |||||||||
Serial crystallography data reduction | Crystal hits: 1817 / Frame hits: 14706 / Frames indexed: 157 / Frames total: 14706 / Lattices indexed: 157 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6XKM Resolution: 2.4→29.59 Å / Cor.coef. Fo:Fc: 0.813 / Cor.coef. Fo:Fc free: 0.752 / SU B: 15.264 / SU ML: 0.282 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.46 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 197.02 Å2 / Biso mean: 39.221 Å2 / Biso min: 2.54 Å2
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Refinement step | Cycle: final / Resolution: 2.4→29.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.403→2.465 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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