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- PDB-9mg2: Structure of Kluyveromyces lactis mRNA cap (guanine-N7) methyltra... -

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Basic information

Entry
Database: PDB / ID: 9mg2
TitleStructure of Kluyveromyces lactis mRNA cap (guanine-N7) methyltransferase, Abd1, in complex with sinefungin
ComponentsmRNA cap guanine-N(7) methyltransferase
KeywordsTRANSFERASE / METHYLTRANSFERASE / MRNA / CAP / sinefungin / 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 / SINEFUNGIN / mRNA cap guanine-N(7) methyltransferase
Similarity search - Component
Biological speciesKluyveromyces lactis NRRL Y-1140 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 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)67,97913
Polymers66,5542
Non-polymers1,42611
Water7,260403
1
A: mRNA cap guanine-N(7) methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1979
Polymers33,2771
Non-polymers9208
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)33,7824
Polymers33,2771
Non-polymers5063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.962, 54.789, 112.933
Angle α, β, γ (deg.)90.00, 92.80, 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 , 5 types, 414 molecules

#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: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / 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-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / 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: 2.13 Å3/Da / Density % sol: 42.36 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Magesium Chloride, and 25% (w/v) PEG 3350

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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: 1.59→50 Å / Num. obs: 67709 / % possible obs: 89.6 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.058 / Χ2: 1.126 / Net I/σ(I): 9.5 / Num. measured all: 143857
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.59-1.622.10.52534011.257191.7
1.62-1.652.10.48834381.241190.9
1.65-1.682.10.41933921.248192.1
1.68-1.712.10.37834371.243189.5
1.71-1.752.10.32133971.229191.5
1.75-1.792.10.27133841.192189.7
1.79-1.842.10.23133511.286188.6
1.84-1.892.10.19533441.294189.3
1.89-1.942.10.15433191.221188.1
1.94-22.10.12332791.042187.2
2-2.072.10.11832661.336187.4
2.07-2.162.10.08832591.133186.2
2.16-2.262.20.07432390.825185.8
2.26-2.382.10.07232161.029184.9
2.38-2.522.10.0632510.931186.4
2.52-2.722.10.05432610.949185.8
2.72-2.992.10.04533450.937188.1
2.99-3.432.10.03735380.998192.9
3.43-4.322.10.0337171.015197.7
4.32-502.20.02738751.11198.4

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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: 1.59→24.64 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2187 3363 4.97 %
Rwork0.1868 --
obs0.1884 67646 89.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.59→24.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4676 0 97 403 5176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.796
X-RAY DIFFRACTIONf_dihedral_angle_d17.181893
X-RAY DIFFRACTIONf_chiral_restr0.054687
X-RAY DIFFRACTIONf_plane_restr0.006867
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.610.29811410.2562626X-RAY DIFFRACTION90
1.61-1.640.31711420.25092717X-RAY DIFFRACTION91
1.64-1.660.31261570.24612714X-RAY DIFFRACTION92
1.66-1.690.30381260.23662710X-RAY DIFFRACTION91
1.69-1.720.25111470.22312671X-RAY DIFFRACTION90
1.72-1.750.26271580.21252689X-RAY DIFFRACTION91
1.75-1.780.23961490.20572673X-RAY DIFFRACTION89
1.78-1.820.2291240.20112669X-RAY DIFFRACTION90
1.82-1.860.2351200.20242637X-RAY DIFFRACTION89
1.86-1.90.26991410.20452689X-RAY DIFFRACTION89
1.9-1.950.2481470.19252582X-RAY DIFFRACTION87
1.95-20.2361300.18862608X-RAY DIFFRACTION87
2-2.060.24671280.1932606X-RAY DIFFRACTION88
2.06-2.130.22071350.18222584X-RAY DIFFRACTION86
2.13-2.20.20121190.17722580X-RAY DIFFRACTION86
2.2-2.290.21721280.18542578X-RAY DIFFRACTION86
2.29-2.40.22111390.18992545X-RAY DIFFRACTION86
2.4-2.520.21121310.19362571X-RAY DIFFRACTION86
2.52-2.680.24131370.19292587X-RAY DIFFRACTION86
2.68-2.890.24471510.19932606X-RAY DIFFRACTION87
2.89-3.180.22421500.19612699X-RAY DIFFRACTION91
3.18-3.640.19391600.17752875X-RAY DIFFRACTION95
3.64-4.580.17791380.15523014X-RAY DIFFRACTION98
4.58-24.640.16681650.15773053X-RAY DIFFRACTION98

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