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Yorodumi- PDB-8cet: Crystal structure of monkeypox virus methyltransferase VP39 in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cet | ||||||
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Title | Crystal structure of monkeypox virus methyltransferase VP39 in complex with inhibitor TO507 | ||||||
Components | Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase | ||||||
Keywords | VIRAL PROTEIN / viral / methyltransferase / vp39 / monkeypox / mpox / capping / enzyme / inhibitor | ||||||
Function / homology | Function and homology information regulation of mRNA 3'-end processing / 7-methylguanosine mRNA capping / translation elongation factor activity / virion component / methyltransferase cap1 / mRNA (nucleoside-2'-O-)-methyltransferase activity Similarity search - Function | ||||||
Biological species | Monkeypox virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Klima, M. / Silhan, J. / Boura, E. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Discovery and structural characterization of monkeypox virus methyltransferase VP39 inhibitors reveal similarities to SARS-CoV-2 nsp14 methyltransferase. Authors: Silhan, J. / Klima, M. / Otava, T. / Skvara, P. / Chalupska, D. / Chalupsky, K. / Kozic, J. / Nencka, R. / Boura, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cet.cif.gz | 138.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cet.ent.gz | 98.7 KB | Display | PDB format |
PDBx/mmJSON format | 8cet.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cet_validation.pdf.gz | 855.1 KB | Display | wwPDB validaton report |
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Full document | 8cet_full_validation.pdf.gz | 860 KB | Display | |
Data in XML | 8cet_validation.xml.gz | 21 KB | Display | |
Data in CIF | 8cet_validation.cif.gz | 28.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ce/8cet ftp://data.pdbj.org/pub/pdb/validation_reports/ce/8cet | HTTPS FTP |
-Related structure data
Related structure data | 8b07C 8ceqC 8cerC 8cesC 8cevC 8cgbC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 35949.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Monkeypox virus Gene: PAPS, MPXV-M2940_FCT-085, MPXV-M2957_Lagos-085, MPXV-M3021_Delta-085, MPXV-M5312_HM12_Rivers-085, MPXV-M5320_M15_Bayelsa-078, MPXV-Nig_SEV71_2_82-080, MPXV-Singapore-085, MPXV-UK_P1-085, MPXV- ...Gene: PAPS, MPXV-M2940_FCT-085, MPXV-M2957_Lagos-085, MPXV-M3021_Delta-085, MPXV-M5312_HM12_Rivers-085, MPXV-M5320_M15_Bayelsa-078, MPXV-Nig_SEV71_2_82-080, MPXV-Singapore-085, MPXV-UK_P1-085, MPXV-UK_P2-085, MPXV-UK_P3-085, MPXV-W_Nigeria-080, MPXV297957_076, MPXV298464_067, PDLMKLCO_00090 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0F6N8X1, methyltransferase cap1 #2: Chemical | #3: Water | ChemComp-HOH / | 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: 2.34 Å3/Da / Density % sol: 47.52 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 200 mM lithium citrate, 14.5% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 11, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→44.19 Å / Num. obs: 21106 / % possible obs: 87.19 % / Redundancy: 5.9 % / Biso Wilson estimate: 36.71 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.1501 / Rpim(I) all: 0.06444 / Rrim(I) all: 0.1642 / Net I/σ(I): 10.59 |
Reflection shell | Resolution: 2.5→2.589 Å / Redundancy: 4.8 % / Rmerge(I) obs: 1.12 / Mean I/σ(I) obs: 1.36 / Num. unique obs: 1836 / CC1/2: 0.71 / CC star: 0.911 / Rpim(I) all: 0.5113 / Rrim(I) all: 1.24 / % possible all: 76.65 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→44.19 Å / SU ML: 0.3657 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.649 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.29 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→44.19 Å
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Refine LS restraints |
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LS refinement shell |
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