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- PDB-9mg0: Structure of Kluyveromyces lactis mRNA cap (guanine-N7) methyltra... -

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Basic information

Entry
Database: PDB / ID: 9mg0
TitleStructure of Kluyveromyces lactis mRNA cap (guanine-N7) methyltransferase, Abd1, in complex with SAH
ComponentsmRNA cap guanine-N(7) methyltransferase
KeywordsTRANSFERASE / METHYLTRANSFERASE / MRNA / CAP / SAH / Abd1 / K. lactis
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
DI(HYDROXYETHYL)ETHER / S-ADENOSYL-L-HOMOCYSTEINE / mRNA cap guanine-N(7) methyltransferase
Similarity search - Component
Biological speciesKluyveromyces lactis NRRL Y-1140 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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

Downloads & links

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Assembly

Deposited unit
A: mRNA cap guanine-N(7) methyltransferase
B: mRNA cap guanine-N(7) methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,70628
Polymers66,5542
Non-polymers2,15326
Water10,359575
1
A: mRNA cap guanine-N(7) methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,28412
Polymers33,2771
Non-polymers1,00711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: mRNA cap guanine-N(7) methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,42216
Polymers33,2771
Non-polymers1,14515
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.616, 64.821, 73.524
Angle α, β, γ (deg.)90.00, 94.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein mRNA cap guanine-N(7) methyltransferase / mRNA (guanine-N(7))-methyltransferase / mRNA cap methyltransferase


Mass: 33276.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis NRRL Y-1140 (yeast)
Gene: ABD1, KLLA0F10527g / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q6CKI0, mRNA (guanine-N7)-methyltransferase

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Non-polymers , 6 types, 601 molecules

#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


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


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 575 / 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: 2.27 Å3/Da / Density % sol: 45.83 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Calcium Chloride, 20% (w/v) PEG 3350, and 0.1 M Potassium Sodium Tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 143920 / % possible obs: 98.6 % / Redundancy: 4 % / Rmerge(I) obs: 0.059 / Χ2: 1.216 / Net I/σ(I): 12.4 / Num. measured all: 576584
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.3-1.323.90.70270681.425197.2
1.32-1.353.90.65670701.4197.4
1.35-1.3740.55971001.409197.8
1.37-1.440.47170861.392197.6
1.4-1.4340.42171211.445198.1
1.43-1.4640.35271911.398198.2
1.46-1.540.2871301.37198.5
1.5-1.5440.22671691.349198.6
1.54-1.5940.1872011.288198.7
1.59-1.6440.16171921.282198.9
1.64-1.740.13671991.236199.1
1.7-1.7640.1172471.183199.3
1.76-1.844.10.08972461.107199.5
1.84-1.9440.07472731.048199.7
1.94-2.064.10.06672891.043199.8
2.06-2.224.10.0673251199.9
2.22-2.4540.04873001.076199.8
2.45-2.83.90.03772901.009199.6
2.8-3.534.10.03273500.986199.7
3.53-5040.0370730.95194.5

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5156)refinement
Aimlessdata scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→24.96 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1867 7303 5.08 %
Rwork0.1654 --
obs0.1665 143728 98.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→24.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4676 0 116 575 5367
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.992
X-RAY DIFFRACTIONf_dihedral_angle_d17.2361938
X-RAY DIFFRACTIONf_chiral_restr0.081713
X-RAY DIFFRACTIONf_plane_restr0.014897
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.310.34682030.31464130X-RAY DIFFRACTION90
1.31-1.330.28822180.30114491X-RAY DIFFRACTION97
1.33-1.350.28622330.28484478X-RAY DIFFRACTION97
1.35-1.360.26742310.25944517X-RAY DIFFRACTION97
1.36-1.380.23962190.24124531X-RAY DIFFRACTION98
1.38-1.40.28642370.23664484X-RAY DIFFRACTION98
1.4-1.420.26482110.22674569X-RAY DIFFRACTION98
1.42-1.440.23862380.21384573X-RAY DIFFRACTION98
1.44-1.460.24572250.20554485X-RAY DIFFRACTION98
1.46-1.490.23242070.19664553X-RAY DIFFRACTION98
1.49-1.510.19382260.18294585X-RAY DIFFRACTION98
1.51-1.540.1962490.17594503X-RAY DIFFRACTION99
1.54-1.570.18632540.17034522X-RAY DIFFRACTION99
1.57-1.60.17832510.16474577X-RAY DIFFRACTION99
1.6-1.640.1862550.16634569X-RAY DIFFRACTION99
1.64-1.680.17952180.16474586X-RAY DIFFRACTION99
1.68-1.720.1822480.15824602X-RAY DIFFRACTION99
1.72-1.760.18062120.15024570X-RAY DIFFRACTION99
1.76-1.820.16642860.15684588X-RAY DIFFRACTION99
1.82-1.870.19092920.15184538X-RAY DIFFRACTION99
1.87-1.940.17512590.15154598X-RAY DIFFRACTION100
1.94-2.020.15522320.14424623X-RAY DIFFRACTION100
2.02-2.110.1632440.14884647X-RAY DIFFRACTION100
2.11-2.220.16412610.13794634X-RAY DIFFRACTION100
2.22-2.360.16032600.14844585X-RAY DIFFRACTION100
2.36-2.540.1732650.1514624X-RAY DIFFRACTION100
2.54-2.80.19122950.15434590X-RAY DIFFRACTION99
2.8-3.20.17732660.15814623X-RAY DIFFRACTION100
3.2-4.030.15872580.15094637X-RAY DIFFRACTION99
4.03-24.960.2082500.16054413X-RAY DIFFRACTION93

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