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- PDB-6w4h: 1.80 Angstrom Resolution Crystal Structure of NSP16 - NSP10 Compl... -
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Basic information
Entry | Database: PDB / ID: 6w4h | ||||||
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Title | 1.80 Angstrom Resolution Crystal Structure of NSP16 - NSP10 Complex from SARS-CoV-2 | ||||||
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![]() | VIRAL PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / nsp16 / nsp10 / complex | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Minasov, G. / Shuvalova, L. / Rosas-Lemus, M. / Kiryukhina, O. / Wiersum, G. / Godzik, A. / Jaroszewski, L. / Stogios, P.J. / Skarina, T. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
![]() | ![]() 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. #1: Journal: Biorxiv / Year: 2020 Title: The crystal structure of nsp10-nsp16 heterodimer from SARS-CoV-2 in complex with S-adenosylmethionine. Authors: Rosas-Lemus, M. / Minasov, G. / Shuvalova, L. / Inniss, N.L. / Kiryukhina, O. / Wiersum, G. / Kim, Y. / Jedrzejczak, R. / Maltseva, N.I. / Endres, M. / Jaroszewski, L. / Godzik, A. / ...Authors: Rosas-Lemus, M. / Minasov, G. / Shuvalova, L. / Inniss, N.L. / Kiryukhina, O. / Wiersum, G. / Kim, Y. / Jedrzejczak, R. / Maltseva, N.I. / Endres, M. / Jaroszewski, L. / Godzik, A. / Joachimiak, A. / Satchell, K.J.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 205.6 KB | Display | ![]() |
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PDB format | ![]() | 161.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 23.1 KB | Display | |
Data in CIF | ![]() | 34.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6w75C ![]() 6wjtC ![]() 6wkqC ![]() 6wq3C ![]() 6wrzC ![]() 6wvnC ![]() 3r24S S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Experimental dataset #1 | Data reference: ![]() |
Other databases |
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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 / Fragment: UNP residues 6799-7096 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 / Fragment: UNP residues 4254-4392 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: rep, 1a-1b / Plasmid: pMCSG53 / Production host: ![]() ![]() |
-Sugars , 1 types, 2 molecules ![](data/chem/img/BDF.gif)
#6: Sugar |
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-Non-polymers , 5 types, 448 molecules ![](data/chem/img/SO3.gif)
![](data/chem/img/SAM.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SAM.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-SO3 / | ||||
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#4: Chemical | ChemComp-SAM / | ||||
#5: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.33 Å3/Da / Density % sol: 71.6 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 5.3 mg/mL 1:1 nsp16/nsp10 in 0.15 M sodium chloride, 0.01 M Tris, pH 7.5, 2 mM SAM, 1 mM TCEP, 5% glycerol against ComPAS screen A7 (0.2 M calcium acetate, 0.1 M HEPES, pH 7.5, 18% w/v PEG ...Details: 5.3 mg/mL 1:1 nsp16/nsp10 in 0.15 M sodium chloride, 0.01 M Tris, pH 7.5, 2 mM SAM, 1 mM TCEP, 5% glycerol against ComPAS screen A7 (0.2 M calcium acetate, 0.1 M HEPES, pH 7.5, 18% w/v PEG 8000), cryoprotectant: 1:1 screen + 50% sucrose |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 7, 2020 / Details: C(111) |
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 77886 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.024 / Rrim(I) all: 0.065 / Rsym value: 0.06 / Χ2: 1.007 / Net I/σ(I): 29.3 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.765 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 3873 / CC1/2: 0.762 / CC star: 0.93 / Rpim(I) all: 0.313 / Rrim(I) all: 0.828 / Rsym value: 0.765 / Χ2: 0.992 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3R24 Resolution: 1.8→29.76 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.962 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.07 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: 115.28 Å2 / Biso mean: 31.531 Å2 / Biso min: 15.7 Å2
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Refinement step | Cycle: final / Resolution: 1.8→29.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 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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