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- PDB-9mg3: Structure of Kluyveromyces lactis mRNA cap (guanine-N7) methyltra... -

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Basic information

Entry
Database: PDB / ID: 9mg3
TitleStructure of Kluyveromyces lactis mRNA cap (guanine-N7) methyltransferase, Abd1, in complex with sinefungin and GTP
ComponentsmRNA cap guanine-N(7) methyltransferase
KeywordsTRANSFERASE / METHYLTRANSFERASE / MRNA / CAP / sinefungin / GTP / 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
GUANOSINE-5'-TRIPHOSPHATE / SINEFUNGIN / mRNA cap guanine-N(7) methyltransferase
Similarity search - Component
Biological speciesKluyveromyces lactis NRRL Y-1140 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 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. / Almo, S.C. / Shuman, S. / Ghosh, A.
History
DepositionDec 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2025Group: Database references / Category: citation_author
Revision 1.2Aug 6, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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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)69,32125
Polymers66,5542
Non-polymers2,76823
Water9,044502
1
A: mRNA cap guanine-N(7) methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,64712
Polymers33,2771
Non-polymers1,37011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: mRNA cap guanine-N(7) methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,67513
Polymers33,2771
Non-polymers1,39812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.043, 92.611, 101.298
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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, 525 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-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / 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: 2.29 Å3/Da / Density % sol: 46.34 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.18 M Lithium Sulfate, 29.5% (w/v) PEG 4000, and 0.1 M Tris

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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: 1.42→50 Å / Num. obs: 114595 / % possible obs: 99.3 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.086 / Χ2: 1.128 / Net I/σ(I): 10.8 / Num. measured all: 837533
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.42-1.444.90.8753781.217193.6
1.44-1.475.60.72155451.216198.1
1.47-1.570.61556691.212199.5
1.5-1.537.40.50356781.24199.5
1.53-1.567.40.42557021.233199.7
1.56-1.67.40.37157151.229199.8
1.6-1.647.40.33156881.249199.7
1.64-1.687.40.28357151.229199.9
1.68-1.737.40.2457101.211199.8
1.73-1.797.40.20357261.187199.9
1.79-1.857.40.17157661.161199.8
1.85-1.937.40.14456871.142199.9
1.93-2.017.50.1257761.072199.9
2.01-2.127.60.1157301.0261100
2.12-2.257.70.09558011.0671100
2.25-2.437.80.08757701.0451100
2.43-2.6780.08558081.0521100
2.67-3.067.90.07658580.955199.9
3.06-3.857.60.05958670.986199.5
3.85-507.70.04860060.955197.8

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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: 1.42→39.96 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2008 5644 4.94 %
Rwork0.1736 --
obs0.175 114206 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.42→39.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4686 0 169 502 5357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d1.099
X-RAY DIFFRACTIONf_dihedral_angle_d19.2371929
X-RAY DIFFRACTIONf_chiral_restr0.081704
X-RAY DIFFRACTIONf_plane_restr0.009886
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.440.30341740.30343217X-RAY DIFFRACTION90
1.44-1.450.30641850.2853457X-RAY DIFFRACTION95
1.45-1.470.28312010.27163493X-RAY DIFFRACTION98
1.47-1.490.25221950.24343575X-RAY DIFFRACTION99
1.49-1.510.28761770.22823614X-RAY DIFFRACTION99
1.51-1.530.22941730.21893557X-RAY DIFFRACTION99
1.53-1.550.1931630.1933633X-RAY DIFFRACTION99
1.55-1.580.2191840.20583598X-RAY DIFFRACTION99
1.58-1.60.26031820.1993629X-RAY DIFFRACTION99
1.6-1.630.24251810.1913601X-RAY DIFFRACTION99
1.63-1.660.21061830.18853614X-RAY DIFFRACTION100
1.66-1.690.20871850.18663610X-RAY DIFFRACTION100
1.69-1.720.21522030.18163632X-RAY DIFFRACTION99
1.72-1.750.20941760.17723606X-RAY DIFFRACTION100
1.75-1.790.20161740.173614X-RAY DIFFRACTION100
1.79-1.830.20632000.1723611X-RAY DIFFRACTION100
1.83-1.880.22951900.17653647X-RAY DIFFRACTION100
1.88-1.930.22332000.18073605X-RAY DIFFRACTION100
1.93-1.990.19221830.16223662X-RAY DIFFRACTION100
1.99-2.050.20661920.16373636X-RAY DIFFRACTION100
2.05-2.120.18731820.16473639X-RAY DIFFRACTION100
2.12-2.210.19731900.15713674X-RAY DIFFRACTION100
2.21-2.310.17952060.15453660X-RAY DIFFRACTION100
2.31-2.430.18781930.15863654X-RAY DIFFRACTION100
2.43-2.580.19071920.16063681X-RAY DIFFRACTION100
2.58-2.780.19171930.16763670X-RAY DIFFRACTION100
2.78-3.060.24471900.17183719X-RAY DIFFRACTION100
3.06-3.510.1931850.1713719X-RAY DIFFRACTION100
3.51-4.420.16752160.14963703X-RAY DIFFRACTION99
4.42-39.960.17651960.17353832X-RAY DIFFRACTION98

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