+Open data
-Basic information
Entry | Database: PDB / ID: 8cgb | |||||||||
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Title | Monkeypox virus VP39 in complex with SAH | |||||||||
Components | Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase | |||||||||
Keywords | TRANSFERASE / Methyltransferase / Ligand / Monkeypox virus | |||||||||
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: 2.47 Å | |||||||||
Authors | Silhan, J. / Klima, M. / Skvara, P. / Boura, E. | |||||||||
Funding support | European Union, Czech Republic, 2items
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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 | 8cgb.cif.gz | 134.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cgb.ent.gz | 102.4 KB | Display | PDB format |
PDBx/mmJSON format | 8cgb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cgb_validation.pdf.gz | 730.8 KB | Display | wwPDB validaton report |
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Full document | 8cgb_full_validation.pdf.gz | 738.4 KB | Display | |
Data in XML | 8cgb_validation.xml.gz | 23.9 KB | Display | |
Data in CIF | 8cgb_validation.cif.gz | 33.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cg/8cgb ftp://data.pdbj.org/pub/pdb/validation_reports/cg/8cgb | HTTPS FTP |
-Related structure data
Related structure data | 8b07C 8ceqC 8cerC 8cesC 8cetC 8cevC 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) / Strain (production host): BL21 / References: UniProt: A0A0F6N8X1, methyltransferase cap1 #2: Chemical | ChemComp-SAH / | #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: 2.55 Å3/Da / Density % sol: 51.69 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: Lithium Citrate, 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: Dec 20, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.47→49.57 Å / Num. obs: 25226 / % possible obs: 99.87 % / Redundancy: 13.2 % / Biso Wilson estimate: 35.1 Å2 / CC1/2: 0.978 / CC star: 0.994 / Rmerge(I) obs: 0.5451 / Rpim(I) all: 0.1544 / Rrim(I) all: 0.567 / Net I/σ(I): 5.67 |
Reflection shell | Resolution: 2.472→2.56 Å / Redundancy: 13.7 % / Rmerge(I) obs: 3.1 / Mean I/σ(I) obs: 0.82 / Num. unique obs: 2453 / CC1/2: 0.423 / CC star: 0.771 / Rpim(I) all: 0.8603 / Rrim(I) all: 3.219 / % possible all: 99.84 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.47→49.57 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.45 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.47→49.57 Å
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Refine LS restraints |
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LS refinement shell |
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