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- PDB-8b07: Crystal structure of monkeypox virus methyltransferase VP39 in co... -

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Basic information

Entry
Database: PDB / ID: 8b07
TitleCrystal structure of monkeypox virus methyltransferase VP39 in complex with sinefungin
ComponentsCap-specific mRNA (nucleoside-2'-O-)-methyltransferase
KeywordsVIRAL PROTEIN / viral / methyltransferase / vp39 / monkeypox / capping / enzyme
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
SINEFUNGIN / Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase
Similarity search - Component
Biological speciesMonkeypox virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsSilhan, J. / Klima, M. / 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
DepositionSep 7, 2022Deposition 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 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6624
Polymers71,8992
Non-polymers7632
Water6,395355
1
A: Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3312
Polymers35,9491
Non-polymers3811
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)36,3312
Polymers35,9491
Non-polymers3811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.891, 84.427, 153.755
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-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N7O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 47.48 %
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: Sep 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.05→49.17 Å / Num. obs: 43138 / % possible obs: 99.82 % / Redundancy: 13.1 % / Biso Wilson estimate: 29.19 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.2726 / Rpim(I) all: 0.07762 / Rrim(I) all: 0.2836 / Net I/σ(I): 9.82
Reflection shellResolution: 2.05→2.125 Å / Redundancy: 13.4 % / Rmerge(I) obs: 2.276 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4205 / CC1/2: 0.448 / CC star: 0.786 / Rpim(I) all: 0.6401 / Rrim(I) all: 2.366 / % possible all: 98.52

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHASER2.8.3phasing
Coot0.9.6model building
PHENIX1.20_4459refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VP3

1vp3


Resolution: 2.05→49.17 Å / SU ML: 0.2501 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.989
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2327 2157 5 %random selection
Rwork0.2084 40959 --
obs0.2096 43116 99.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.11 Å2
Refinement stepCycle: LAST / Resolution: 2.05→49.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4686 0 54 355 5095
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00264867
X-RAY DIFFRACTIONf_angle_d0.51866599
X-RAY DIFFRACTIONf_chiral_restr0.0423727
X-RAY DIFFRACTIONf_plane_restr0.0047850
X-RAY DIFFRACTIONf_dihedral_angle_d13.06451835
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10.34121390.32842625X-RAY DIFFRACTION97.77
2.1-2.150.35071420.28912715X-RAY DIFFRACTION100
2.15-2.210.32961420.26272679X-RAY DIFFRACTION100
2.21-2.270.29781420.2622699X-RAY DIFFRACTION99.96
2.27-2.350.27181420.25192707X-RAY DIFFRACTION100
2.35-2.430.28851420.23672691X-RAY DIFFRACTION100
2.43-2.530.28421420.24132697X-RAY DIFFRACTION100
2.53-2.640.25221430.23532716X-RAY DIFFRACTION100
2.64-2.780.25691420.21912707X-RAY DIFFRACTION99.96
2.78-2.960.24591440.22222730X-RAY DIFFRACTION100
2.96-3.190.25871440.21442742X-RAY DIFFRACTION99.97
3.19-3.510.22591450.19232752X-RAY DIFFRACTION100
3.51-4.010.17851460.17882768X-RAY DIFFRACTION100
4.01-5.060.17531470.15012790X-RAY DIFFRACTION100
5.06-49.170.19941550.1952941X-RAY DIFFRACTION99.77

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