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

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Basic information

Entry
Database: PDB / ID: 8cev
TitleCrystal structure of monkeypox virus methyltransferase VP39 in complex with inhibitor TO1119
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-UG9 / Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase
Similarity search - Component
Biological speciesMonkeypox virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 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)72,9184
Polymers71,8992
Non-polymers1,0192
Water4,558253
1
A: Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4592
Polymers35,9491
Non-polymers5091
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)36,4592
Polymers35,9491
Non-polymers5091
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.282, 84.511, 155.049
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-UG9 / (2~{S})-2-azanyl-4-[[(2~{S},3~{S},4~{R},5~{R})-5-(4-azanyl-5-iodanyl-pyrrolo[2,3-d]pyrimidin-7-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanyl]butanoic acid


Mass: 509.319 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H20IN5O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.38 Å3/Da / Density % sol: 48.36 %
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: 2.14→44.46 Å / Num. obs: 38720 / % possible obs: 99.81 % / Redundancy: 13.2 % / Biso Wilson estimate: 31.93 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.2984 / Rpim(I) all: 0.08485 / Rrim(I) all: 0.3105 / Net I/σ(I): 7.97
Reflection shellResolution: 2.14→2.216 Å / Redundancy: 12.8 % / Rmerge(I) obs: 2.541 / Mean I/σ(I) obs: 1.09 / Num. unique obs: 3793 / CC1/2: 0.494 / CC star: 0.813 / Rpim(I) all: 0.7284 / Rrim(I) all: 2.645 / % possible all: 99.58

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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: 2.14→44.46 Å / SU ML: 0.2771 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5956
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2444 1935 5 %random selection
Rwork0.2127 36764 --
obs0.2143 38699 99.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.62 Å2
Refinement stepCycle: LAST / Resolution: 2.14→44.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4595 0 54 253 4902
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214780
X-RAY DIFFRACTIONf_angle_d0.48046481
X-RAY DIFFRACTIONf_chiral_restr0.0403715
X-RAY DIFFRACTIONf_plane_restr0.0048816
X-RAY DIFFRACTIONf_dihedral_angle_d11.8871799
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.190.36771350.30862565X-RAY DIFFRACTION99.45
2.19-2.250.30181370.2932593X-RAY DIFFRACTION99.85
2.25-2.320.31441360.26732588X-RAY DIFFRACTION99.96
2.32-2.390.34751360.27352590X-RAY DIFFRACTION99.93
2.39-2.480.30491370.26262599X-RAY DIFFRACTION99.85
2.48-2.580.29971350.26042572X-RAY DIFFRACTION99.89
2.58-2.70.28381370.24762604X-RAY DIFFRACTION99.96
2.7-2.840.27111390.22842623X-RAY DIFFRACTION99.93
2.84-3.020.25651380.22612626X-RAY DIFFRACTION99.96
3.02-3.250.2411370.21822615X-RAY DIFFRACTION99.82
3.25-3.580.23721390.19822633X-RAY DIFFRACTION100
3.58-4.090.2161400.18172663X-RAY DIFFRACTION99.79
4.09-5.160.18431410.15822677X-RAY DIFFRACTION99.93
5.16-44.460.21031480.19582816X-RAY DIFFRACTION99.33

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