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Open data
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Basic information
Entry | Database: PDB / ID: 7nh7 | ||||||
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Title | OC43 coronavirus methyltransferase | ||||||
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![]() | VIRAL PROTEIN / coronavirus / methyltransferase | ||||||
Function / homology | ![]() RNA exonuclease activity / : / host cell membrane / DNA helicase activity / viral genome replication / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / SARS coronavirus main proteinase / host cell endoplasmic reticulum-Golgi intermediate compartment ...RNA exonuclease activity / : / host cell membrane / DNA helicase activity / viral genome replication / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / SARS coronavirus main proteinase / host cell endoplasmic reticulum-Golgi intermediate compartment / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / methylation / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / DNA helicase / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / membrane => GO:0016020 / Hydrolases; Acting on ester bonds / RNA helicase activity / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / zinc ion binding / ATP binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Dostalik, P. / Krafcikova, P. / Boura, E. | ||||||
![]() | ![]() Title: OC43 coronavirus methyltransferase Authors: Dostalik, P. / Krafcikova, P. / Boura, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110.9 KB | Display | ![]() |
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PDB format | ![]() | 76.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 537.8 KB | Display | ![]() |
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Full document | ![]() | 542 KB | Display | |
Data in XML | ![]() | 20.7 KB | Display | |
Data in CIF | ![]() | 29.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6yz1S S: Starting model for refinement |
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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
#1: Protein | Mass: 33453.527 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P0C6X6, ubiquitinyl hydrolase 1, SARS coronavirus main proteinase, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, RNA-directed RNA polymerase, DNA ...References: UniProt: P0C6X6, ubiquitinyl hydrolase 1, SARS coronavirus main proteinase, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, RNA-directed RNA polymerase, DNA helicase, RNA helicase, Transferases; Transferring one-carbon groups; Methyltransferases, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters, Hydrolases; Acting on ester bonds | ||||
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#2: Protein | Mass: 13097.088 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P0C6U7, ubiquitinyl hydrolase 1, SARS coronavirus main proteinase, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases | ||||
#3: Chemical | ChemComp-SFG / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: JSCG screen |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Feb 1, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5419 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→38.35 Å / Num. obs: 23828 / % possible obs: 99.74 % / Redundancy: 5.1 % / Biso Wilson estimate: 24.8 Å2 / CC1/2: 0.981 / Rmerge(I) obs: 0.1305 / Net I/σ(I): 11.66 |
Reflection shell | Resolution: 2.2→2.28 Å / Mean I/σ(I) obs: 2.48 / Num. unique obs: 2385 / CC1/2: 0.687 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6YZ1 Resolution: 2.2→38.35 Å / SU ML: 0.2341 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 20.9983 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→38.35 Å
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Refine LS restraints |
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LS refinement shell |
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