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- PDB-8ces: Crystal structure of monkeypox virus methyltransferase VP39 in co... -

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Basic information

Entry
Database: PDB / ID: 8ces
TitleCrystal structure of monkeypox virus methyltransferase VP39 in complex with inhibitor TO500
ComponentsCap-specific mRNA (nucleoside-2'-O-)-methyltransferase
KeywordsVIRAL 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 / 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
Chem-UH2 / Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase
Similarity search - Component
Biological speciesMonkeypox virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKlima, M. / Silhan, J. / Boura, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: 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
DepositionFeb 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1May 3, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)72,9464
Polymers71,8992
Non-polymers1,0472
Water75742
1
A: Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4732
Polymers35,9491
Non-polymers5241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4732
Polymers35,9491
Non-polymers5241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.606, 84.055, 154.054
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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: Chemical ChemComp-UH2 / (2~{S})-2-azanyl-4-[[(2~{S},3~{S},4~{R},5~{R})-5-[4-azanyl-5-[2-(1~{H}-benzimidazol-2-yl)ethynyl]pyrrolo[2,3-d]pyrimidin-7-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanyl]butanoic acid


Mass: 523.564 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H25N7O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.32 Å3/Da / Density % sol: 47.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 200 mM lithium citrate, 14.5% (w/v) 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 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.5→48.93 Å / Num. obs: 22141 / % possible obs: 91.12 % / Redundancy: 6.2 % / Biso Wilson estimate: 37.9 Å2 / CC1/2: 0.99 / CC star: 0.998 / Rmerge(I) obs: 0.1896 / Rpim(I) all: 0.08119 / Rrim(I) all: 0.207 / Net I/σ(I): 8.47
Reflection shellResolution: 2.5→2.589 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.239 / Mean I/σ(I) obs: 1.27 / Num. unique obs: 1864 / CC1/2: 0.558 / CC star: 0.846 / Rpim(I) all: 0.5534 / Rrim(I) all: 1.365 / % possible all: 78.45

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Processing

Software
NameVersionClassification
XDSxdsapp v3.0data reduction
XDSxdsapp v3.0data scaling
PHASER2.8.3phasing
Coot0.9.6model building
PHENIX1.20_4459refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→48.93 Å / SU ML: 0.3733 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.7717
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2818 1094 5.01 %random selection
Rwork0.2358 20746 --
obs0.238 21840 91.14 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.05 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4548 0 74 42 4664
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00464750
X-RAY DIFFRACTIONf_angle_d0.69246450
X-RAY DIFFRACTIONf_chiral_restr0.0449713
X-RAY DIFFRACTIONf_plane_restr0.0063817
X-RAY DIFFRACTIONf_dihedral_angle_d12.85351780
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.610.39731170.30592218X-RAY DIFFRACTION79.26
2.61-2.750.38191220.31522306X-RAY DIFFRACTION82.14
2.75-2.920.35951300.26682455X-RAY DIFFRACTION88.44
2.92-3.150.28121380.262637X-RAY DIFFRACTION94.16
3.15-3.470.32261440.27532734X-RAY DIFFRACTION96.35
3.47-3.970.32761380.28152611X-RAY DIFFRACTION91.48
3.97-50.21191480.16892814X-RAY DIFFRACTION98.44
5-48.930.22111570.19072971X-RAY DIFFRACTION98.15

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