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- PDB-8jed: Crystal structure of mRNA cap (guanine-N7) methyltransferase E12 ... -

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Basic information

Entry
Database: PDB / ID: 8jed
TitleCrystal structure of mRNA cap (guanine-N7) methyltransferase E12 subunit from monkeypox virus and discovery of its inhibitors
ComponentsmRNA-capping enzyme regulatory subunit OPG124
KeywordsTRANSFERASE / monkeypox virus / N7-methyltransferase E12 subunit / inhibitors
Function / homologyPoxvirus mRNA capping enzyme, small subunit / Poxvirus mRNA capping enzyme, small subunit superfamily / Poxvirus mRNA capping enzyme, small subunit / virion component / DNA-templated transcription termination / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / mRNA-capping enzyme regulatory subunit OPG124
Function and homology information
Biological speciesMonkeypox virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsWang, D. / Zhao, R. / Shu, W. / Hu, W. / Wang, M. / Cao, J. / Zhou, X.
Funding support China, 5items
OrganizationGrant numberCountry
Other government2020XM01
Other government1331KFC
National Natural Science Foundation of China (NSFC)81801858 China
National Natural Science Foundation of China (NSFC)82170523 China
Other government202103021224234
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: Crystal structure of mRNA cap (guanine-N7) methyltransferase E12 subunit from monkeypox virus and discovery of its inhibitors.
Authors: Wang, D.P. / Zhao, R. / Wang, H.F. / Wang, M.Y. / Hu, W.S. / Lin, M.M. / Shu, W. / Sun, Y.J. / Cao, J.M. / Cui, W. / Zhou, X.
History
DepositionMay 15, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: mRNA-capping enzyme regulatory subunit OPG124


Theoretical massNumber of molelcules
Total (without water)34,6641
Polymers34,6641
Non-polymers00
Water3,207178
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.251, 46.407, 62.526
Angle α, β, γ (deg.)90.00, 90.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein mRNA-capping enzyme regulatory subunit OPG124 / Virus termination factor small subunit / mRNA-capping enzyme 33 kDa subunit / mRNA-capping enzyme ...Virus termination factor small subunit / mRNA-capping enzyme 33 kDa subunit / mRNA-capping enzyme D12 subunit / mRNA-capping enzyme small subunit


Mass: 34663.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monkeypox virus / Gene: OPG124, MPXVgp109 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7H0DN96
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O

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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: 2.23 Å3/Da / Density % sol: 44.81 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium chloride, 0.1 M bis-tris propane pH 9.0, 25% w/v polyethylene glycol 1,500

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Data collection

DiffractionMean temperature: 289.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Nov 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.16→53.25 Å / Num. obs: 16534 / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 7.6
Reflection shellResolution: 2.16→2.28 Å / Rmerge(I) obs: 0.473 / Num. unique obs: 16493

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata scaling
XDSdata reduction
PHENIXphasing
PDB_EXTRACT3.27data extraction
REFMAC5.8.0267refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.16→40.69 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2541 807 4.89 %
Rwork0.1997 --
obs0.2023 16494 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.16→40.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2423 0 0 178 2601
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0012421
X-RAY DIFFRACTIONf_angle_d0.4143270
X-RAY DIFFRACTIONf_dihedral_angle_d14.389899
X-RAY DIFFRACTIONf_chiral_restr0.037368
X-RAY DIFFRACTIONf_plane_restr0.003408
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.30.31111190.2562596X-RAY DIFFRACTION99
2.3-2.480.31911330.23282596X-RAY DIFFRACTION100
2.48-2.730.30821460.22572586X-RAY DIFFRACTION100
2.73-3.120.26911380.21082609X-RAY DIFFRACTION100
3.12-3.930.22561430.17832610X-RAY DIFFRACTION100
3.93-40.690.2111280.17452690X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.19560.96341.51650.66890.24741.6812-0.06790.17790.0727-0.07760.0871-0.1042-0.13910.06420.00810.16380.00870.01490.15480.0020.1564-13.88912.949-18.599
24.6527-1.78093.08510.8268-0.99813.07920.0943-0.3611-0.35530.02870.13680.09970.1394-0.2588-0.25790.1995-0.0209-0.00020.17060.04220.1765-24.2050.211-10.932
36.21240.030.99431.78710.05564.7134-0.0328-0.5545-0.00610.30350.0092-0.0122-0.2008-0.19210.06020.13150.02280.01810.1664-0.03010.1162-34.61610.177-10.973
41.89590.50311.32321.02030.57071.9867-0.0035-0.04180.00540.01040.0152-0.03980.02470.00960.0350.12440.00970.02370.08450.01660.1288-17.5677.984-13.514
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 1:47 )B1 - 47
2X-RAY DIFFRACTION2( CHAIN B AND RESID 48:102 )B48 - 102
3X-RAY DIFFRACTION3( CHAIN B AND RESID 103:117 )B103 - 117
4X-RAY DIFFRACTION4( CHAIN B AND RESID 125:292 )B125 - 292

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