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

ID or keywords:

Entry

Database: PDB / ID: 9mg5

Title

Structure of Saccharomyces cerevisiae mRNA cap (guanine-N7) methyltransferase, Abd1, in complex with sinefungin and GTP

Components

mRNA cap guanine-N7 methyltransferase

Keywords

TRANSFERASE / 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

Biological species

Saccharomyces cerevisiae YJM789 (yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.45 Å

Authors

Nilson, D.J. / Fedorov, E. / Ghosh, A.

Funding support

United States, 2items

Organization	Grant number	Country
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

Citation

Journal: 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

Deposition	Dec 10, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 9, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9mg5.cif.gz	406.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9mg5.ent.gz	338 KB	Display	PDB format
PDBx/mmJSON format	9mg5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9mg5_validation.pdf.gz	2.1 MB	Display	wwPDB validaton report
Full document	9mg5_full_validation.pdf.gz	2.1 MB	Display
Data in XML	9mg5_validation.xml.gz	34.8 KB	Display
Data in CIF	9mg5_validation.cif.gz	49.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mg/9mg5 ftp://data.pdbj.org/pub/pdb/validation_reports/mg/9mg5	HTTPS FTP

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Related structure data

Related structure data	9mg0C 9mg1C 9mg2C 9mg3C 9mg4C 9mg6C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#145 - Jan 2012 Messenger RNA Capping similarity (6) #103 - Jul 2008 Dengue Virus similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1) #197 - May 2016 Zika Virus similarity (1)

Deposited unit

A: mRNA cap guanine-N7 methyltransferase

B: mRNA cap guanine-N7 methyltransferase

hetero molecules

78.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: mRNA cap guanine-N7 methyltransferase

hetero molecules

defined by author&software
Evidence: gel filtration, Superdex S200
39.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: mRNA cap guanine-N7 methyltransferase

hetero molecules

defined by author&software
39.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	173
Space group name H-M	P6₃

Components on special symmetry positions

ID	Model	Components
1	1	B-861- HOH

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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 interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.31 Å³/Da / Density % sol: 46.77 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.98 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection twin	Operator: h,-h-k,-l / Fraction: 0.422
Reflection	Resolution: 1.45→29.87 Å / Num. obs: 183124 / % possible obs: 99.9 % / Redundancy: 17.5 % / CC_1/2: 0.99 / Net I/σ(I): 6.3
Reflection shell	Resolution: 1.45→1.47 Å / R_merge(I) obs: 0.8 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 111696 / CC_1/2: 0.85 / CC star: 0.84

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Processing

Software

Name	Version	Classification
PHENIX	(1.21.2_5419	refinement
pointless		data scaling
HKL-2000		data reduction
PHASER		phasing

Refinement

Method 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

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1266	5922	5.04 %	RANDOM
R_work	0.1075	-	-	-
obs	0.1177	117568	99.02 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.45→29.87 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4818	0	276	531	5625

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008
X-RAY DIFFRACTION	f_angle_d	1.103
X-RAY DIFFRACTION	f_dihedral_angle_d	19.122	2119
X-RAY DIFFRACTION	f_chiral_restr	0.078	742
X-RAY DIFFRACTION	f_plane_restr	0.007	914

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.45-1.47	0.2006	296	0.1772	5255	X-RAY DIFFRACTION	89
1.47-1.5	0.1914	295	0.1663	5400	X-RAY DIFFRACTION	92
1.5-1.53	0.1837	280	0.1596	5476	X-RAY DIFFRACTION	92
1.53-1.56	0.1625	305	0.1527	5494	X-RAY DIFFRACTION	93
1.56-1.59	0.1479	304	0.1455	5547	X-RAY DIFFRACTION	93
1.59-1.63	0.1477	295	0.1408	5538	X-RAY DIFFRACTION	94
1.63-1.67	0.1492	304	0.1357	5573	X-RAY DIFFRACTION	94
1.67-1.72	0.1675	285	0.13	5575	X-RAY DIFFRACTION	95
1.72-1.77	0.1419	302	0.1257	5652	X-RAY DIFFRACTION	95
1.77-1.83	0.125	300	0.1225	5609	X-RAY DIFFRACTION	95
1.83-1.89	0.1222	277	0.1158	5645	X-RAY DIFFRACTION	95
1.89-1.97	0.122	283	0.1063	5627	X-RAY DIFFRACTION	95
1.97-2.06	0.1232	297	0.1013	5631	X-RAY DIFFRACTION	95
2.06-2.16	0.1183	286	0.1006	5661	X-RAY DIFFRACTION	95
2.16-2.3	0.113	302	0.0923	5642	X-RAY DIFFRACTION	95
2.3-2.48	0.101	310	0.0862	5639	X-RAY DIFFRACTION	95
2.48-2.73	0.1144	287	0.0922	5665	X-RAY DIFFRACTION	95
2.73-3.12	0.1224	296	0.1026	5645	X-RAY DIFFRACTION	95
3.12-3.93	0.1568	264	0.1282	5703	X-RAY DIFFRACTION	96
3.93-29.87	0.1384	312	0.1248	5711	X-RAY DIFFRACTION	95

Refinement TLS params.

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

ID	L11 (°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)
1	0.5898	-0.1922	0.0615	1.1278	-0.2883	0.5796	0.0222	0.0703	-0.1054	-0.0514	-0.0575	-0.0366	0.0759	0.0862	0.0335	0.0723	0.0211	0.0128	0.0825	-0.0011	0.1348	20.1918	28.0372	-35.0641
2	2.205	-0.3374	-0.5069	1.4834	0.5634	1.6964	0.0378	0.0347	0.1195	0.0228	0.1217	-0.1359	-0.002	0.2085	-0.1451	0.0935	-0.0134	0.009	0.1359	0.0052	0.2442	34.5781	50.149	-35.2667
3	2.0522	0.0175	-0.1562	0.6319	-0.0718	0.6597	-0.0197	0.0273	-0.1438	-0.0444	-0.0286	0.0283	0.0616	-0.0043	0.0371	0.0719	0.0043	0	0.0561	0.0047	0.1384	10.7088	34.8066	-33.3245
4	3.0837	0.8955	0.0312	1.9972	-0.019	1.6393	0.0221	0.1575	-0.0818	-0.0163	0.0029	-0.2213	0.0001	0.1445	-0.0088	0.0713	0.0188	0.0014	0.0586	0.0071	0.1565	26.9624	11.8259	2.1927
5	0.7013	0.8038	0.5976	4.4449	-1.0014	1.6048	-0.0341	0.0874	-0.1193	-0.0192	-0.0124	-0.2209	0.0187	0.1399	0.0471	0.0797	-0.0011	0.0099	0.0655	-0.0114	0.1504	15.6866	7.8013	-5.5947
6	0.7736	0.2995	0.2092	2.3997	-0.6778	2.1115	-0.0792	0.179	-0.1753	-0.3283	0.0534	-0.3434	0.1655	0.2489	0.0106	0.1523	-0.0121	0.0367	0.1236	-0.0337	0.1731	18.084	10.8796	-15.2104
7	0.6371	0.3687	0.0884	1.1441	0.1646	0.4166	-0.0675	0.1023	0.082	-0.0842	0.0343	0.1511	-0.0337	-0.0421	0.034	0.0691	-0.0122	-0.0081	0.0683	0.0103	0.1457	8.2247	19.9368	-4.0793
8	0.8799	0.7405	0.0523	3.341	-0.1572	1.1112	0.0836	-0.0452	0.161	0.2326	-0.0747	-0.0737	-0.0839	0.0502	0.0003	0.1023	-0.0148	-0.0023	0.0779	-0.0133	0.1535	25.423	36.9448	12.5569
9	0.7805	0.3701	0.1184	1.3174	0.1154	0.4145	-0.0021	-0.0397	0.0682	0.0173	-0.0145	0.013	-0.0404	0.0434	0.0152	0.0795	-0.008	-0.0067	0.0602	0.0023	0.1313	20.4397	32.5075	5.2922
10	1.7592	-1.3283	0.2537	1.0149	-0.0783	1.102	-0.0651	-0.2324	-0.3075	0.1049	0.0259	0.0789	0.1487	0.0082	0.0233	0.0935	-0.0063	0.0102	0.0708	0.0171	0.1534	19.6989	12.3156	12.1139
11	1.8745	-0.0424	0.1867	1.9178	0.1757	1.5839	-0.0121	-0.0531	-0.0696	0.0641	0.0739	-0.0078	0.0168	0.124	-0.0076	0.091	0.0175	-0.0215	0.1108	-0.0006	0.2399	34.4054	5.1612	7.515
12	4.6386	0.851	1.1667	0.9908	0.4746	1.009	0.0419	-0.119	-0.1112	0.1089	-0.0294	-0.1614	0.0237	0.0555	-0.0363	0.0725	0.0015	-0.0082	0.0441	-0.0011	0.1438	22.8145	19.332	8.306
13	5.257	-2.8203	-0.0919	4.201	-0.4965	1.824	0.182	0.2241	0.2897	-0.2212	-0.1989	0.0245	-0.118	-0.1749	0.0175	0.0886	-0.0053	0.0273	0.1212	-0.0169	0.2583	-10.4125	22.7579	0.809
14	2.7561	-0.8943	-0.2965	1.5375	0.4978	1.6495	0.0334	-0.1626	-0.0034	0.0815	-0.0153	-0.2807	0.0003	0.2302	-0.012	0.0665	-0.0219	-0.0117	0.0938	0.0387	0.183	27.0243	43.44	-29.8739
15	0.8429	-0.4483	-0.3554	3.6502	-0.6025	1.3521	-0.0479	-0.0217	0.1242	0.0701	-0.0385	-0.1949	-0.042	0.1269	0.0932	0.0885	-0.0092	-0.0124	0.062	0.008	0.124	15.7447	47.4901	-21.9102
16	1.7899	-0.566	0.0408	1.717	0.2015	1.8243	-0.1879	-0.1765	0.1923	0.3666	0.1206	-0.2371	-0.021	0.1797	0.0387	0.1657	0.0203	-0.0362	0.111	-0.002	0.1472	18.1994	44.5048	-12.6436
17	0.8167	-0.5575	-0.0563	1.2172	0.1304	0.3811	-0.0715	-0.1056	-0.1004	0.1107	0.0498	0.1357	0.0409	-0.0215	0.0179	0.0755	0.0053	0.0143	0.077	0.0208	0.1357	8.2264	35.4206	-23.5893
18	1.3891	-1.45	-0.0068	4.1933	-0.4653	1.2199	0.1757	0.1531	-0.1173	-0.3845	-0.1758	-0.1257	0.1477	0.1131	-0.0023	0.1311	0.0658	0.0197	0.1358	-0.0059	0.1695	25.3276	18.6904	-41.2089

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 304 through 382 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 383 through 405 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 406 through 435 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 141 through 161 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 162 through 188 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 189 through 221 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 222 through 285 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 286 through 303 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 304 through 363 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 364 through 382 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 383 through 405 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 406 through 423 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 424 through 436 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 141 through 161 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 162 through 188 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 189 through 221 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 222 through 285 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 286 through 303 )

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