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Yorodumi- PDB-6xkm: Room Temperature Structure of SARS-CoV-2 NSP10/NSP16 Methyltransf... -
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Basic information
| Entry | Database: PDB / ID: 6xkm | |||||||||
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| Title | Room Temperature Structure of SARS-CoV-2 NSP10/NSP16 Methyltransferase in a Complex with SAM Determined by Fixed-Target Serial Crystallography | |||||||||
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Keywords | VIRAL PROTEIN / SARS CoV-2 / Serial Crystallography / Methyltransferase / S-Adenosylmethionine / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | |||||||||
| Function / homology | Function and homology informationprotein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / TRAF3-dependent IRF activation pathway / ISG15-specific peptidase activity ...protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / TRAF3-dependent IRF activation pathway / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / snRNP Assembly / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease activity / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated suppression of host NF-kappaB cascade / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / regulation of autophagy / viral protein processing / host cell perinuclear region of cytoplasm / lyase activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / copper ion binding / viral translational frameshifting / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 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 | ![]() | |||||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | |||||||||
Authors | Wilamowski, M. / Sherrell, D.A. / Minasov, G. / Kim, Y. / Shuvalova, L. / Lavens, A. / Chard, R. / Rosas-Lemus, M. / Maltseva, N. / Jedrzejczak, R. ...Wilamowski, M. / Sherrell, D.A. / Minasov, G. / Kim, Y. / 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: 2021Title: 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: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 6xkm.cif.gz | 184.8 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb6xkm.ent.gz | 143.5 KB | Display | PDB format |
| PDBx/mmJSON format | 6xkm.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 6xkm_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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| Full document | 6xkm_full_validation.pdf.gz | 1.6 MB | Display | |
| Data in XML | 6xkm_validation.xml.gz | 17.3 KB | Display | |
| Data in CIF | 6xkm_validation.cif.gz | 24.4 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xk/6xkm ftp://data.pdbj.org/pub/pdb/validation_reports/xk/6xkm | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 7jheC ![]() 7jibC ![]() 7jpeC ![]() 6w4hS 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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| 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.) ![]() Gene: rep, 1a-1b / Plasmid: pMCSG53 / Production host: ![]() 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.) ![]() Gene: rep, 1a-1b / Production host: ![]() |
-Non-polymers , 4 types, 132 molecules 






| #3: Chemical | ChemComp-CL / | ||
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| #4: Chemical | ChemComp-SAM / | ||
| #5: Chemical | | #6: 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: 4.49 Å3/Da / Density % sol: 72.6 % |
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| Crystal grow | Temperature: 295 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 ul ...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 polypropylene tube. |
-Data collection
| Diffraction | Mean temperature: 295 K / Serial crystal experiment: Y |
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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: Jun 12, 2020 Details: Sagittally focusing mono and vertically focusing mirror |
| 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: 2.25→49.57 Å / Num. obs: 41770 / % possible obs: 100 % / Redundancy: 82.41 % / Biso Wilson estimate: 23.2 Å2 / CC1/2: 0.968 / Net I/σ(I): 2.68 |
| Reflection shell | Resolution: 2.25→2.29 Å / Redundancy: 10.24 % / Mean I/σ(I) obs: 0.58 / Num. unique obs: 2090 / CC1/2: 0.449 / % possible all: 99.7 |
| Serial crystallography sample delivery | Description: Nylon Mesh / Method: fixed target |
| Serial crystallography sample delivery fixed target | Crystals per unit: 1 / Description: SBC Mesh Holder / Details: start/stop raster over area / Motion control: SmarAct Motors via PMAC / Sample dehydration prevention: 6 um Mylar sandwich / Sample holding: 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 Sample unit size: 90 µm / Support base: xyz stage / Velocity horizontal: 10 / Velocity vertical: 10 |
| Serial crystallography data reduction | Crystal hits: 10990 / Frame hits: 73100 / Frames indexed: 10990 / Frames total: 73100 / Lattices indexed: 7951 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: 6W4H Resolution: 2.25→49.57 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.938 / SU B: 21.5 / SU ML: 0.214 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.142 / 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: 131.13 Å2 / Biso mean: 37.635 Å2 / Biso min: 6.36 Å2
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| Refinement step | Cycle: final / Resolution: 2.25→49.57 Å
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| Refine LS restraints |
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| LS refinement shell | Resolution: 2.25→2.308 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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