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- PDB-9mg6: Structure of Saccharomyces cerevisiae mRNA cap (guanine-N7) methy... -

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Basic information

Entry
Database: PDB / ID: 9mg6
TitleStructure of Saccharomyces cerevisiae mRNA cap (guanine-N7) methyltransferase variant, Abd1-K163R-K311R-F387Y-Y416F, in complex with sinefungin and GTP
ComponentsmRNA cap guanine-N7 methyltransferase
KeywordsTRANSFERASE / METHYLTRANSFERASE / MRNA / CAP / SAH / Abd1 / S. cerevisiae
Function / homology
Function and homology information


mRNA (guanine-N7)-methyltransferase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA binding / nucleus
Similarity search - Function
mRNA cap guanine-N7 methyltransferase, eukaryotes / mRNA cap guanine-N7 methyltransferase / mRNA (guanine-N(7))-methyltransferase domain / mRNA (guanine-N(7))-methyltransferase domain / mRNA (guanine-N(7)-)-methyltransferase (EC 2.1.1.56) domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / SINEFUNGIN / mRNA cap guanine-N(7) methyltransferase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae YJM789 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsNilson, D.J. / Ghosh, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5T32GM007491 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Structural basis for sensitivity and acquired resistance of fungal cap guanine-N7 methyltransferases to the antifungal antibiotic Sinefungin
Authors: Nilson, D.J. / Schwer, B. / Shuman, S. / Almo, S.C.
History
DepositionDec 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mRNA cap guanine-N7 methyltransferase
B: mRNA cap guanine-N7 methyltransferase
C: mRNA cap guanine-N7 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,02326
Polymers102,8133
Non-polymers4,21123
Water4,324240
1
A: mRNA cap guanine-N7 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6228
Polymers34,2711
Non-polymers1,3517
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: mRNA cap guanine-N7 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6849
Polymers34,2711
Non-polymers1,4138
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: mRNA cap guanine-N7 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7189
Polymers34,2711
Non-polymers1,4478
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.779, 201.170, 160.532
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein mRNA cap guanine-N7 methyltransferase


Mass: 34270.867 Da / Num. of mol.: 3 / Mutation: K163R, K311R, F387Y, Y416F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae YJM789 (yeast)
Gene: ABD1, SCY_0445 / Variant: K163R / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A6ZLH5, mRNA (guanine-N7)-methyltransferase

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Non-polymers , 5 types, 263 molecules

#2: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H23N7O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 4.47 Å3/Da / Density % sol: 72.47 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2 M Ammonium Sulphate, 1.8% Ethylene Glycol, 100 mM Tris-HCl, 10 mM Tris(2-carboxyethl)phosphine hydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.73→17.99 Å / Num. obs: 48851 / % possible obs: 99.3 % / Redundancy: 5.2 % / CC1/2: 0.983 / Rmerge(I) obs: 0.194 / Rpim(I) all: 0.093 / Rrim(I) all: 0.216 / Χ2: 1 / Net I/σ(I): 6.8
Reflection shellResolution: 2.73→2.82 Å / % possible obs: 97.3 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.801 / Num. measured all: 23477 / Num. unique obs: 4380 / CC1/2: 0.719 / Rpim(I) all: 0.375 / Rrim(I) all: 0.886 / Χ2: 1.03 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→17.98 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.92 / SU B: 19.183 / SU ML: 0.186 / Cross valid method: FREE R-VALUE / ESU R: 0.397 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21523 2269 5 %RANDOM
Rwork0.17806 ---
obs0.17991 43152 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.183 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20 Å20 Å2
2--0.63 Å20 Å2
3----1.58 Å2
Refinement stepCycle: 1 / Resolution: 2.8→17.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7163 0 258 243 7664
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0127599
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166885
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.83710299
X-RAY DIFFRACTIONr_angle_other_deg0.5271.75715885
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2185882
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.175546
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.169101226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0680.21070
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028773
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021828
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3513.2133546
X-RAY DIFFRACTIONr_mcbond_other2.3473.2133546
X-RAY DIFFRACTIONr_mcangle_it3.9295.7674422
X-RAY DIFFRACTIONr_mcangle_other3.935.7684423
X-RAY DIFFRACTIONr_scbond_it3.4463.7454053
X-RAY DIFFRACTIONr_scbond_other3.4073.7174002
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6566.6945800
X-RAY DIFFRACTIONr_long_range_B_refined8.20430.828160
X-RAY DIFFRACTIONr_long_range_B_other8.16330.838151
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 182 -
Rwork0.265 3091 -
obs--99.67 %

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