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- PDB-9mg5: Structure of Saccharomyces cerevisiae mRNA cap (guanine-N7) methy... -

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Basic information

Entry
Database: PDB / ID: 9mg5
TitleStructure of Saccharomyces cerevisiae mRNA cap (guanine-N7) methyltransferase, Abd1, 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 / DI(HYDROXYETHYL)ETHER / SINEFUNGIN / mRNA cap guanine-N(7) methyltransferase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae YJM789 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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-N7 methyltransferase
B: mRNA cap guanine-N7 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,39540
Polymers74,0002
Non-polymers4,39538
Water9,548530
1
A: mRNA cap guanine-N7 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,15619
Polymers37,0001
Non-polymers2,15618
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: mRNA cap guanine-N7 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,23921
Polymers37,0001
Non-polymers2,23920
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.732, 95.732, 129.256
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11B-861-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein mRNA cap guanine-N7 methyltransferase


Mass: 36999.957 Da / Num. of mol.: 2
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

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Non-polymers , 8 types, 568 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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 530 / 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: 2.31 Å3/Da / Density % sol: 46.77 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Ammonium Sulphate, and 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.422
ReflectionResolution: 1.45→29.87 Å / Num. obs: 183124 / % possible obs: 99.9 % / Redundancy: 17.5 % / CC1/2: 0.99 / Net I/σ(I): 6.3
Reflection shellResolution: 1.45→1.47 Å / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 111696 / CC1/2: 0.85 / CC star: 0.84

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419refinement
pointlessdata scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→29.87 Å / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.97 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.1266 5922 5.04 %RANDOM
Rwork0.1075 ---
obs0.1177 117568 99.02 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4818 0 276 531 5625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d1.103
X-RAY DIFFRACTIONf_dihedral_angle_d19.1222119
X-RAY DIFFRACTIONf_chiral_restr0.078742
X-RAY DIFFRACTIONf_plane_restr0.007914
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.470.20062960.17725255X-RAY DIFFRACTION89
1.47-1.50.19142950.16635400X-RAY DIFFRACTION92
1.5-1.530.18372800.15965476X-RAY DIFFRACTION92
1.53-1.560.16253050.15275494X-RAY DIFFRACTION93
1.56-1.590.14793040.14555547X-RAY DIFFRACTION93
1.59-1.630.14772950.14085538X-RAY DIFFRACTION94
1.63-1.670.14923040.13575573X-RAY DIFFRACTION94
1.67-1.720.16752850.135575X-RAY DIFFRACTION95
1.72-1.770.14193020.12575652X-RAY DIFFRACTION95
1.77-1.830.1253000.12255609X-RAY DIFFRACTION95
1.83-1.890.12222770.11585645X-RAY DIFFRACTION95
1.89-1.970.1222830.10635627X-RAY DIFFRACTION95
1.97-2.060.12322970.10135631X-RAY DIFFRACTION95
2.06-2.160.11832860.10065661X-RAY DIFFRACTION95
2.16-2.30.1133020.09235642X-RAY DIFFRACTION95
2.3-2.480.1013100.08625639X-RAY DIFFRACTION95
2.48-2.730.11442870.09225665X-RAY DIFFRACTION95
2.73-3.120.12242960.10265645X-RAY DIFFRACTION95
3.12-3.930.15682640.12825703X-RAY DIFFRACTION96
3.93-29.870.13843120.12485711X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5898-0.19220.06151.1278-0.28830.57960.02220.0703-0.1054-0.0514-0.0575-0.03660.07590.08620.03350.07230.02110.01280.0825-0.00110.134820.191828.0372-35.0641
22.205-0.3374-0.50691.48340.56341.69640.03780.03470.11950.02280.1217-0.1359-0.0020.2085-0.14510.0935-0.01340.0090.13590.00520.244234.578150.149-35.2667
32.05220.0175-0.15620.6319-0.07180.6597-0.01970.0273-0.1438-0.0444-0.02860.02830.0616-0.00430.03710.07190.004300.05610.00470.138410.708834.8066-33.3245
43.08370.89550.03121.9972-0.0191.63930.02210.1575-0.0818-0.01630.0029-0.22130.00010.1445-0.00880.07130.01880.00140.05860.00710.156526.962411.82592.1927
50.70130.80380.59764.4449-1.00141.6048-0.03410.0874-0.1193-0.0192-0.0124-0.22090.01870.13990.04710.0797-0.00110.00990.0655-0.01140.150415.68667.8013-5.5947
60.77360.29950.20922.3997-0.67782.1115-0.07920.179-0.1753-0.32830.0534-0.34340.16550.24890.01060.1523-0.01210.03670.1236-0.03370.173118.08410.8796-15.2104
70.63710.36870.08841.14410.16460.4166-0.06750.10230.082-0.08420.03430.1511-0.0337-0.04210.0340.0691-0.0122-0.00810.06830.01030.14578.224719.9368-4.0793
80.87990.74050.05233.341-0.15721.11120.0836-0.04520.1610.2326-0.0747-0.0737-0.08390.05020.00030.1023-0.0148-0.00230.0779-0.01330.153525.42336.944812.5569
90.78050.37010.11841.31740.11540.4145-0.0021-0.03970.06820.0173-0.01450.013-0.04040.04340.01520.0795-0.008-0.00670.06020.00230.131320.439732.50755.2922
101.7592-1.32830.25371.0149-0.07831.102-0.0651-0.2324-0.30750.10490.02590.07890.14870.00820.02330.0935-0.00630.01020.07080.01710.153419.698912.315612.1139
111.8745-0.04240.18671.91780.17571.5839-0.0121-0.0531-0.06960.06410.0739-0.00780.01680.124-0.00760.0910.0175-0.02150.1108-0.00060.239934.40545.16127.515
124.63860.8511.16670.99080.47461.0090.0419-0.119-0.11120.1089-0.0294-0.16140.02370.0555-0.03630.07250.0015-0.00820.0441-0.00110.143822.814519.3328.306
135.257-2.8203-0.09194.201-0.49651.8240.1820.22410.2897-0.2212-0.19890.0245-0.118-0.17490.01750.0886-0.00530.02730.1212-0.01690.2583-10.412522.75790.809
142.7561-0.8943-0.29651.53750.49781.64950.0334-0.1626-0.00340.0815-0.0153-0.28070.00030.2302-0.0120.0665-0.0219-0.01170.09380.03870.18327.024343.44-29.8739
150.8429-0.4483-0.35543.6502-0.60251.3521-0.0479-0.02170.12420.0701-0.0385-0.1949-0.0420.12690.09320.0885-0.0092-0.01240.0620.0080.12415.744747.4901-21.9102
161.7899-0.5660.04081.7170.20151.8243-0.1879-0.17650.19230.36660.1206-0.2371-0.0210.17970.03870.16570.0203-0.03620.111-0.0020.147218.199444.5048-12.6436
170.8167-0.5575-0.05631.21720.13040.3811-0.0715-0.1056-0.10040.11070.04980.13570.0409-0.02150.01790.07550.00530.01430.0770.02080.13578.226435.4206-23.5893
181.3891-1.45-0.00684.1933-0.46531.21990.17570.1531-0.1173-0.3845-0.1758-0.12570.14770.1131-0.00230.13110.06580.01970.1358-0.00590.169525.327618.6904-41.2089
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 304 through 382 )
2X-RAY DIFFRACTION2chain 'B' and (resid 383 through 405 )
3X-RAY DIFFRACTION3chain 'B' and (resid 406 through 435 )
4X-RAY DIFFRACTION4chain 'A' and (resid 141 through 161 )
5X-RAY DIFFRACTION5chain 'A' and (resid 162 through 188 )
6X-RAY DIFFRACTION6chain 'A' and (resid 189 through 221 )
7X-RAY DIFFRACTION7chain 'A' and (resid 222 through 285 )
8X-RAY DIFFRACTION8chain 'A' and (resid 286 through 303 )
9X-RAY DIFFRACTION9chain 'A' and (resid 304 through 363 )
10X-RAY DIFFRACTION10chain 'A' and (resid 364 through 382 )
11X-RAY DIFFRACTION11chain 'A' and (resid 383 through 405 )
12X-RAY DIFFRACTION12chain 'A' and (resid 406 through 423 )
13X-RAY DIFFRACTION13chain 'A' and (resid 424 through 436 )
14X-RAY DIFFRACTION14chain 'B' and (resid 141 through 161 )
15X-RAY DIFFRACTION15chain 'B' and (resid 162 through 188 )
16X-RAY DIFFRACTION16chain 'B' and (resid 189 through 221 )
17X-RAY DIFFRACTION17chain 'B' and (resid 222 through 285 )
18X-RAY DIFFRACTION18chain 'B' and (resid 286 through 303 )

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