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

ID or keywords:

Entry

Database: PDB / ID: 9mg3

Title

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

Components

mRNA cap guanine-N(7) methyltransferase

Keywords

TRANSFERASE / 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

Biological species

Kluyveromyces lactis NRRL Y-1140 (yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.42 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

-
Download

PDBx/mmCIF format	9mg3.cif.gz	367.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9mg3.ent.gz	302.5 KB	Display	PDB format
PDBx/mmJSON format	9mg3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9mg3_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	9mg3_full_validation.pdf.gz	1.6 MB	Display
Data in XML	9mg3_validation.xml.gz	34.3 KB	Display
Data in CIF	9mg3_validation.cif.gz	48.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mg/9mg3 ftp://data.pdbj.org/pub/pdb/validation_reports/mg/9mg3	HTTPS FTP

-
Related structure data

Related structure data	9mg0C 9mg1C 9mg2C 9mg4C 9mg5C 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

-
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-N(7) methyltransferase

B: mRNA cap guanine-N(7) methyltransferase

hetero molecules

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

1

A: mRNA cap guanine-N(7) methyltransferase

hetero molecules

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

2

B: mRNA cap guanine-N(7) methyltransferase

hetero molecules

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

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 number	19
Space group name H-M	P2₁2₁2₁

-
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

#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

-
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

-
Details

Has ligand of interest	Y
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.29 Å³/Da / Density % sol: 46.34 %
Crystal grow	Temperature: 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

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS

/ Beamline: X29A / Wavelength: 1.075 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 5, 2015

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.075 Å / Relative weight: 1

Reflection

Resolution: 1.42→50 Å / Num. obs: 114595 / % possible obs: 99.3 % / Redundancy: 7.3 % / R_merge(I) obs: 0.086 / Χ²: 1.128 / Net I/σ(I): 10.8 / Num. measured all: 837533

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	Χ²	Diffraction-ID	% possible all
1.42-1.44	4.9	0.87	5378	1.217	1	93.6
1.44-1.47	5.6	0.721	5545	1.216	1	98.1
1.47-1.5	7	0.615	5669	1.212	1	99.5
1.5-1.53	7.4	0.503	5678	1.24	1	99.5
1.53-1.56	7.4	0.425	5702	1.233	1	99.7
1.56-1.6	7.4	0.371	5715	1.229	1	99.8
1.6-1.64	7.4	0.331	5688	1.249	1	99.7
1.64-1.68	7.4	0.283	5715	1.229	1	99.9
1.68-1.73	7.4	0.24	5710	1.211	1	99.8
1.73-1.79	7.4	0.203	5726	1.187	1	99.9
1.79-1.85	7.4	0.171	5766	1.161	1	99.8
1.85-1.93	7.4	0.144	5687	1.142	1	99.9
1.93-2.01	7.5	0.12	5776	1.072	1	99.9
2.01-2.12	7.6	0.11	5730	1.026	1	100
2.12-2.25	7.7	0.095	5801	1.067	1	100
2.25-2.43	7.8	0.087	5770	1.045	1	100
2.43-2.67	8	0.085	5808	1.052	1	100
2.67-3.06	7.9	0.076	5858	0.955	1	99.9
3.06-3.85	7.6	0.059	5867	0.986	1	99.5
3.85-50	7.7	0.048	6006	0.955	1	97.8

-
Processing

Software

Name	Version	Classification
PHENIX	(1.21rc1_5156)	refinement
Aimless		data scaling
HKL-2000		data reduction
PHASER		phasing

Refinement

Method 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

	R_factor	Num. reflection	% reflection
R_free	0.2008	5644	4.94 %
R_work	0.1736	-	-
obs	0.175	114206	98.94 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.42→39.96 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4686	0	169	502	5357

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008
X-RAY DIFFRACTION	f_angle_d	1.099
X-RAY DIFFRACTION	f_dihedral_angle_d	19.237	1929
X-RAY DIFFRACTION	f_chiral_restr	0.081	704
X-RAY DIFFRACTION	f_plane_restr	0.009	886

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 (%)
1.42-1.44	0.3034	174	0.3034	3217	X-RAY DIFFRACTION	90
1.44-1.45	0.3064	185	0.285	3457	X-RAY DIFFRACTION	95
1.45-1.47	0.2831	201	0.2716	3493	X-RAY DIFFRACTION	98
1.47-1.49	0.2522	195	0.2434	3575	X-RAY DIFFRACTION	99
1.49-1.51	0.2876	177	0.2282	3614	X-RAY DIFFRACTION	99
1.51-1.53	0.2294	173	0.2189	3557	X-RAY DIFFRACTION	99
1.53-1.55	0.193	163	0.193	3633	X-RAY DIFFRACTION	99
1.55-1.58	0.219	184	0.2058	3598	X-RAY DIFFRACTION	99
1.58-1.6	0.2603	182	0.199	3629	X-RAY DIFFRACTION	99
1.6-1.63	0.2425	181	0.191	3601	X-RAY DIFFRACTION	99
1.63-1.66	0.2106	183	0.1885	3614	X-RAY DIFFRACTION	100
1.66-1.69	0.2087	185	0.1866	3610	X-RAY DIFFRACTION	100
1.69-1.72	0.2152	203	0.1816	3632	X-RAY DIFFRACTION	99
1.72-1.75	0.2094	176	0.1772	3606	X-RAY DIFFRACTION	100
1.75-1.79	0.2016	174	0.17	3614	X-RAY DIFFRACTION	100
1.79-1.83	0.2063	200	0.172	3611	X-RAY DIFFRACTION	100
1.83-1.88	0.2295	190	0.1765	3647	X-RAY DIFFRACTION	100
1.88-1.93	0.2233	200	0.1807	3605	X-RAY DIFFRACTION	100
1.93-1.99	0.1922	183	0.1622	3662	X-RAY DIFFRACTION	100
1.99-2.05	0.2066	192	0.1637	3636	X-RAY DIFFRACTION	100
2.05-2.12	0.1873	182	0.1647	3639	X-RAY DIFFRACTION	100
2.12-2.21	0.1973	190	0.1571	3674	X-RAY DIFFRACTION	100
2.21-2.31	0.1795	206	0.1545	3660	X-RAY DIFFRACTION	100
2.31-2.43	0.1878	193	0.1586	3654	X-RAY DIFFRACTION	100
2.43-2.58	0.1907	192	0.1606	3681	X-RAY DIFFRACTION	100
2.58-2.78	0.1917	193	0.1676	3670	X-RAY DIFFRACTION	100
2.78-3.06	0.2447	190	0.1718	3719	X-RAY DIFFRACTION	100
3.06-3.51	0.193	185	0.171	3719	X-RAY DIFFRACTION	100
3.51-4.42	0.1675	216	0.1496	3703	X-RAY DIFFRACTION	99
4.42-39.96	0.1765	196	0.1735	3832	X-RAY DIFFRACTION	98

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 6 types, 525 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Protein , 1 types, 2 molecules AB

-Non-polymers , 6 types, 525 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 6 types, 525 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi