+Open data
-Basic information
Entry | Database: PDB / ID: 8oiv | ||||||
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Title | Monkeypox virus VP39 in complex with SAH and cap0 | ||||||
Components |
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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 synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å | ||||||
Authors | Skvara, P. / Chalupska, D. / Silhan, J. / Klima, M. / Boura, E. | ||||||
Funding support | European Union, 1items
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Citation | Journal: Antiviral Res. / Year: 2023 Title: Structural basis for RNA-cap recognition and methylation by the mpox methyltransferase VP39. Authors: Skvara, P. / Chalupska, D. / Klima, M. / Kozic, J. / Silhan, J. / Boura, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8oiv.cif.gz | 143 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8oiv.ent.gz | 109.1 KB | Display | PDB format |
PDBx/mmJSON format | 8oiv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/8oiv ftp://data.pdbj.org/pub/pdb/validation_reports/oi/8oiv | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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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: RNA chain | | Mass: 2386.496 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: (CAP) = GTG = mGpppG / Source: (synth.) synthetic construct (others) #3: Chemical | #4: Chemical | ChemComp-GTG / | #5: 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: 47.49 % |
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Crystal grow | Temperature: 293 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: Jan 25, 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: 2.12→44.82 Å / Num. obs: 39875 / % possible obs: 98.63 % / Redundancy: 12.3 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.249 / Rpim(I) all: 0.07285 / Rrim(I) all: 0.2597 / Net I/σ(I): 9.55 |
Reflection shell | Resolution: 2.121→2.197 Å / Redundancy: 10 % / Rmerge(I) obs: 2.168 / Num. unique obs: 3684 / CC1/2: 0.352 / CC star: 0.722 / Rpim(I) all: 0.6918 / Rrim(I) all: 2.283 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→44.82 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.37 / 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: 2.12→44.82 Å
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Refine LS restraints |
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LS refinement shell |
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