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- PDB-9mg4: Structure of Saccharomyces cerevisiae mRNA cap (guanine-N7) methy... -

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Basic information

Entry
Database: PDB / ID: 9mg4
TitleStructure of Saccharomyces cerevisiae mRNA cap (guanine-N7) methyltransferase, Abd1, in complex with SAH
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
ACETATE ION / S-ADENOSYL-L-HOMOCYSTEINE / mRNA cap guanine-N(7) methyltransferase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae YJM789 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsNilson, D.J. / Fedorov, E. / 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)S10 OD020068 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,9326
Polymers34,3021
Non-polymers6305
Water5,639313
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Superdex S200
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.160, 95.160, 248.942
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-789-

HOH

21A-818-

HOH

31A-913-

HOH

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Components

#1: Protein mRNA cap guanine-N7 methyltransferase


Mass: 34301.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae YJM789 (yeast)
Gene: ABD1, SCY_0445 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A6ZLH5, mRNA (guanine-N7)-methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.16 Å3/Da / Density % sol: 61.1 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.8 M Sodium Phosphate, 1.2 M Potassium Phosphate, and 0.1 M Sodium Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.75→24.83 Å / Num. obs: 43915 / % possible obs: 100 % / Redundancy: 11.3 % / CC1/2: 0.989 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.057 / Rrim(I) all: 0.194 / Χ2: 0.82 / Net I/σ(I): 9 / Num. measured all: 494627
Reflection shellResolution: 1.75→1.79 Å / % possible obs: 100 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.606 / Num. measured all: 25862 / Num. unique obs: 2478 / CC1/2: 0.897 / Rpim(I) all: 0.196 / Rrim(I) all: 0.637 / Χ2: 0.62 / Net I/σ(I) obs: 3.2

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5156)refinement
Aimlessdata scaling
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→24.83 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1863 2279 5.19 %
Rwork0.1637 --
obs0.1648 43909 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→24.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2411 0 42 313 2766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.811
X-RAY DIFFRACTIONf_dihedral_angle_d18.278978
X-RAY DIFFRACTIONf_chiral_restr0.054360
X-RAY DIFFRACTIONf_plane_restr0.007452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.24741420.21282566X-RAY DIFFRACTION100
1.79-1.830.22091300.19082590X-RAY DIFFRACTION100
1.83-1.880.22941300.17922580X-RAY DIFFRACTION100
1.88-1.930.19771660.18292521X-RAY DIFFRACTION100
1.93-1.990.21891660.17952580X-RAY DIFFRACTION100
1.99-2.050.20551570.17152539X-RAY DIFFRACTION100
2.05-2.120.21921430.17132585X-RAY DIFFRACTION100
2.12-2.210.18941350.16412612X-RAY DIFFRACTION100
2.21-2.310.17761400.15662576X-RAY DIFFRACTION100
2.31-2.430.17161390.16442599X-RAY DIFFRACTION100
2.43-2.580.18151230.16182611X-RAY DIFFRACTION100
2.58-2.780.21031480.17772589X-RAY DIFFRACTION100
2.78-3.060.17581410.17542620X-RAY DIFFRACTION100
3.06-3.50.17441250.16442658X-RAY DIFFRACTION100
3.5-4.410.16151420.13372653X-RAY DIFFRACTION100
4.41-24.830.16631520.15282751X-RAY DIFFRACTION100

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