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- PDB-8oiv: Monkeypox virus VP39 in complex with SAH and cap0 -

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Basic information

Entry
Database: PDB / ID: 8oiv
TitleMonkeypox virus VP39 in complex with SAH and cap0
Components
  • Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase
  • mGpppGAAAAA
KeywordsTRANSFERASE / Methyltransferase / Ligand / Monkeypox virus
Function / homology
Function and homology information


regulation of mRNA 3'-end processing / 7-methylguanosine mRNA capping / virion component / methylation / methyltransferase cap1 / methyltransferase cap1 activity
Similarity search - Function
mRNA methyltransferase-like / Poxvirus/kinetoplastid-type cap-specific nucleoside 2-O-methyltransferase / Poxvirus cap-specific nucleoside 2-O-methyltransferase / Poly A polymerase regulatory subunit / Poxvirus/kinetoplastid-type ribose 2'-O-methyltransferase (EC 2.1.1.57) family profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE / S-ADENOSYL-L-HOMOCYSTEINE / RNA / Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase
Similarity search - Component
Biological speciesMonkeypox virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsSkvara, P. / Chalupska, D. / Silhan, J. / Klima, M. / Boura, E.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)LX22NPO5103European Union
CitationJournal: 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
DepositionMar 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase
B: Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase
D: mGpppGAAAAA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8586
Polymers74,2853
Non-polymers1,5723
Water4,161231
1
A: Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase
D: mGpppGAAAAA
hetero molecules

B: Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8586
Polymers74,2853
Non-polymers1,5723
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445x-1/2,-y-1/2,-z1
Buried area4760 Å2
ΔGint-15 kcal/mol
Surface area25830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.770, 84.890, 155.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase


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 mGpppGAAAAA


Mass: 2386.496 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: (CAP) = GTG = mGpppG / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GTG / 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE / MRNA CAP ANALOG N7-METHYL GPPPG


Mass: 803.440 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N10O18P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: Lithium citrate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Coot0.9.8.6model building
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.2453 1994 5 %
Rwork0.2059 --
obs0.2079 39860 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.12→44.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4739 118 104 231 5192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025118
X-RAY DIFFRACTIONf_angle_d0.5536981
X-RAY DIFFRACTIONf_dihedral_angle_d13.2562004
X-RAY DIFFRACTIONf_chiral_restr0.042766
X-RAY DIFFRACTIONf_plane_restr0.004869
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.170.36781290.31532437X-RAY DIFFRACTION91
2.17-2.230.29561390.28712644X-RAY DIFFRACTION99
2.23-2.30.31811430.27242717X-RAY DIFFRACTION99
2.3-2.370.28731400.24982669X-RAY DIFFRACTION99
2.37-2.460.30721410.25052685X-RAY DIFFRACTION99
2.46-2.560.34151410.25122670X-RAY DIFFRACTION98
2.56-2.670.27891420.23642690X-RAY DIFFRACTION99
2.67-2.810.26021430.22132733X-RAY DIFFRACTION100
2.81-2.990.2581430.212718X-RAY DIFFRACTION100
2.99-3.220.26171430.21282703X-RAY DIFFRACTION99
3.22-3.540.2171450.19682751X-RAY DIFFRACTION100
3.54-4.060.23191440.17692753X-RAY DIFFRACTION99
4.06-5.110.16441460.14822770X-RAY DIFFRACTION99
5.11-44.820.23211550.19242926X-RAY DIFFRACTION99

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