PDB-37bg: Crystal Structure of Histone-lysine N-methyltransferase from Leis...

ID or keywords:

Entry

Database: PDB / ID: 37bg

Title

Crystal Structure of Histone-lysine N-methyltransferase from Leishmania major in complex with S-ADENOSYLMETHIONINE

Components

Histone-lysine N-methyltransferase, H3 lysine-79 specific

Keywords

TRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Histone-lysine N-methyltransferase / Leishmania major

Function / homology

Function and homology information

histone H3K79 trimethyltransferase activity / histone H3K79 methyltransferase activity / subtelomeric heterochromatin formation / DNA damage checkpoint signaling / methylation / chromosome, telomeric region / DNA repair / nucleus
Similarity search - Function

Biological species

Leishmania major strain Friedlin (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.93 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 1items

Citation

Journal: To be published
Title: Crystal Structure of Histone-lysine N-methyltransferase from Leishmania major in complex with S-ADENOSYLMETHIONINE
Authors: Lanyi Lari, N. / Liu, L. / Lovell, S. / Battaile, K.P.

History

Deposition	Jul 10, 2026	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 22, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	37bg.cif.gz	430.6 KB	Display	PDBx/mmCIF format
PDB format	pdb37bg.ent.gz	350.9 KB	Display	PDB format
PDBx/mmJSON format	37bg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/7b/37bg ftp://data.pdbj.org/pub/pdb/validation_reports/7b/37bg	HTTPS FTP

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Related structure data

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	#139 - Jul 2011 DNA Methyltransferase similarity (1)

Deposited unit

A: Histone-lysine N-methyltransferase, H3 lysine-79 specific

B: Histone-lysine N-methyltransferase, H3 lysine-79 specific

C: Histone-lysine N-methyltransferase, H3 lysine-79 specific

D: Histone-lysine N-methyltransferase, H3 lysine-79 specific

hetero molecules

121 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Histone-lysine N-methyltransferase, H3 lysine-79 specific

hetero molecules

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

2

B: Histone-lysine N-methyltransferase, H3 lysine-79 specific

hetero molecules

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

3

C: Histone-lysine N-methyltransferase, H3 lysine-79 specific

hetero molecules

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

4

D: Histone-lysine N-methyltransferase, H3 lysine-79 specific

hetero molecules

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

Unit cell

Length a, b, c (Å)	69.816, 91.915, 81.797
Angle α, β, γ (deg.)	90.00, 102.67, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Histone-lysine N-methyltransferase, H3 lysine-79 specific / Histone H3-K76 methyltransferase / Histone H3-K79 methyltransferase / Histone-lysine N- ...Histone H3-K76 methyltransferase / Histone H3-K79 methyltransferase / Histone-lysine N-methyltransferase / H3 lysine-76 specific Mass: 29630.020 Da / Num. of mol.: 4 / Fragment: E50-K299 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania major strain Friedlin (eukaryote) Gene: LMJF_07_0025 / Plasmid: LemaA.18205.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4QIU2

#1: Protein

Histone-lysine N-methyltransferase, H3 lysine-79 specific / Histone H3-K76 methyltransferase / Histone H3-K79 methyltransferase / Histone-lysine N- ...

Mass: 29630.020 Da / Num. of mol.: 4 / Fragment: E50-K299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Leishmania major strain Friedlin (eukaryote)
Gene: LMJF_07_0025 / Plasmid: LemaA.18205.a.B2 / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4QIU2

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Non-polymers , 5 types, 617 molecules

#2: Chemical	ChemComp-SAM / S-ADENOSYLMETHIONINE Mass: 398.437 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₅H₂₂N₆O₅S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER Mass: 209.240 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₈H₁₉NO₅ / Comment: pH buffer*YM
#5: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 604 / 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: 2.16 Å³/Da / Density % sol: 43.07 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 27.5% PEG 3350, 0.1M Bis-Tris 5.5, 0.2M NaCl. LemaA.18205.a.B2.PW39520 at 12.4 mg/mL. Crystals soaked with 5 mM SAM, plate 21007 C10 drop 2, Puck: PSL-2811, Cryo: 33% P3350, 0.1M BT 5.5, 0.2M NaCl

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Jun 13, 2026
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 1.93→49.37 Å / Num. obs: 75739 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC_1/2: 0.997 / R_merge(I) obs: 0.145 / R_pim(I) all: 0.06 / R_rim(I) all: 0.157 / Χ²: 1.01 / Net I/σ(I): 8.1 / Num. measured all: 516275
Reflection shell	Resolution: 1.93→1.97 Å / % possible obs: 99.9 % / Redundancy: 5.6 % / R_merge(I) obs: 1.095 / Num. measured all: 24871 / Num. unique obs: 4461 / CC_1/2: 0.728 / R_pim(I) all: 0.504 / R_rim(I) all: 1.21 / Χ²: 1.04 / Net I/σ(I) obs: 1.5

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Processing

Software

Name	Version	Classification
PHENIX	(2.1_6048: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.93→49.37 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.19 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2313	3706	4.9 %
R_work	0.1826	-	-
obs	0.1851	75562	99.71 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.93→49.37 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8067	0	181	604	8852

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	8534
X-RAY DIFFRACTION	f_angle_d	0.914	11579
X-RAY DIFFRACTION	f_dihedral_angle_d	15.733	3253
X-RAY DIFFRACTION	f_chiral_restr	0.051	1260
X-RAY DIFFRACTION	f_plane_restr	0.011	1493

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 (%)
1.93-1.96	0.3719	140	0.3158	2771	X-RAY DIFFRACTION	100
1.96-1.98	0.2806	142	0.2867	2745	X-RAY DIFFRACTION	100
1.98-2.01	0.3013	165	0.2662	2709	X-RAY DIFFRACTION	100
2.01-2.04	0.2957	156	0.2496	2752	X-RAY DIFFRACTION	100
2.04-2.07	0.258	153	0.2162	2739	X-RAY DIFFRACTION	100
2.07-2.11	0.2849	162	0.2141	2732	X-RAY DIFFRACTION	100
2.11-2.14	0.2514	129	0.2095	2767	X-RAY DIFFRACTION	100
2.14-2.18	0.2666	133	0.2052	2785	X-RAY DIFFRACTION	100
2.18-2.22	0.2726	140	0.2006	2735	X-RAY DIFFRACTION	100
2.22-2.27	0.2438	139	0.2002	2772	X-RAY DIFFRACTION	100
2.27-2.32	0.2406	129	0.1893	2775	X-RAY DIFFRACTION	100
2.32-2.37	0.3116	149	0.1946	2734	X-RAY DIFFRACTION	100
2.37-2.43	0.241	125	0.1859	2769	X-RAY DIFFRACTION	100
2.43-2.5	0.2763	152	0.1927	2784	X-RAY DIFFRACTION	100
2.5-2.57	0.2399	150	0.1833	2733	X-RAY DIFFRACTION	100
2.57-2.65	0.2437	123	0.1837	2765	X-RAY DIFFRACTION	99
2.65-2.75	0.2204	106	0.1804	2766	X-RAY DIFFRACTION	100
2.75-2.86	0.2332	132	0.1846	2775	X-RAY DIFFRACTION	100
2.86-2.99	0.2439	151	0.1854	2752	X-RAY DIFFRACTION	100
2.99-3.15	0.2484	133	0.1966	2800	X-RAY DIFFRACTION	100
3.15-3.34	0.2589	138	0.1805	2753	X-RAY DIFFRACTION	100
3.34-3.6	0.2043	154	0.1616	2770	X-RAY DIFFRACTION	100
3.6-3.96	0.2022	143	0.1532	2786	X-RAY DIFFRACTION	100
3.96-4.54	0.1692	162	0.13	2776	X-RAY DIFFRACTION	100
4.54-5.71	0.1797	155	0.1503	2777	X-RAY DIFFRACTION	100
5.71-49.37	0.2182	145	0.1902	2834	X-RAY DIFFRACTION	99

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	0.1019	0.3668	0.5106	4.0501	-0.0227	3.8943	-0.0051	-0.5592	0.8863	0.4312	0.0326	0.0663	-0.1805	0.0697	-0.0262	0.2323	0.0532	0.0414	0.2062	-0.0429	0.4475	-2.5421	18.5915	10.9566
2	2.0829	-1.4062	-1.3139	3.9832	1.0197	2.5688	-0.051	-0.0912	0.3286	-0.0269	0.0604	-0.0882	-0.1439	0.014	0.0078	0.1411	-0.0197	-0.0326	0.147	0.0105	0.3507	12.0052	6.59	2.7431
3	1.5239	-0.3904	-0.1774	2.41	0.5439	2.0759	-0.0603	-0.0642	0.0852	0.1605	0.1488	-0.0353	0.0033	0.1395	-0.0682	0.129	0.0199	0.0096	0.1635	-0.0163	0.2482	11.9766	-5.6869	7.2599
4	2.659	0.6979	-0.6349	1.9365	0.9467	1.8918	-0.0265	0.0257	-0.4013	0.1133	-0.0105	0.5996	0.1584	-0.1596	0.0062	0.1646	0.0203	0.0138	0.1867	0.0204	0.459	-5.506	-7.7492	6.7957
5	4.2789	0.4692	-0.9565	0.0573	-0.13	1.0874	0.0467	0.1966	-0.4132	0.0652	0.2117	0.4919	0.0542	-0.2576	-0.1554	0.1547	-0.0021	0.0414	0.2573	0.0709	0.6571	-17.8799	2.794	4.4024
6	5.4099	1.2173	-2.1573	1.9765	-1.3783	3.2705	-0.0461	-0.0328	-0.0507	0.2062	0.0087	0.4025	0.0055	-0.1263	0.014	0.1619	0.0198	0.0367	0.1642	-0.0185	0.3849	-5.3518	7.4166	6.2695
7	2.7369	1.1547	-1.466	6.4022	-0.6218	8.1303	-0.0601	-0.8751	1.0463	0.5062	-0.0546	0.4179	-0.2412	-0.0511	0.134	0.246	0.0297	0.0039	0.2323	-0.0483	0.396	-11.9774	21.9099	50.8862
8	3.2088	-1.3679	-0.5659	3.3489	1.1986	3.079	0.0162	-0.0133	0.2004	-0.2495	-0.0119	-0.0875	-0.0356	-0.1006	0.0074	0.21	-0.0131	-0.0036	0.1918	0.01	0.2493	2.9586	11.0803	41.9365
9	4.9678	-0.6434	-0.1991	4.4433	0.823	3.9402	0.0991	-0.1996	-0.2588	-0.0895	0.0631	-0.2038	0.0121	0.0206	-0.1707	0.2097	0.0255	-0.0135	0.1822	0.03	0.2619	3.6853	-0.4826	46.499
10	4.519	-1.6061	-0.0268	0.9356	-0.2566	0.6609	0.0444	-0.0314	-0.7201	-0.0488	0.0219	0.4222	0.1173	-0.0445	-0.0636	0.291	-0.0183	-0.0503	0.2657	0.0183	0.4253	-13.5016	-2.1925	45.699
11	3.2698	0.0353	-1.056	2.3202	-0.8504	2.4288	-0.0651	-0.0522	0.0187	-0.0096	0.0317	0.1903	-0.0387	-0.2083	-0.0146	0.195	0.0067	-0.0555	0.295	-0.0202	0.2808	-14.7088	10.9295	45.3954
12	4.4861	-4.9925	1.3481	5.5925	-1.4957	4.0458	-0.163	0.6834	-0.2175	-0.6714	0.0825	-0.4632	0.2471	0.1467	0.052	0.2986	-0.0639	0.0014	0.2192	-0.0509	0.5949	-37.122	1.4383	-10.6153
13	2.3935	-0.7676	0.6913	6.8652	1.1411	0.4852	-0.3399	0.3966	-1.0013	-0.5187	0.4803	-0.637	0.0913	0.2526	-0.1401	0.3414	-0.0251	0.148	0.3194	-0.1615	0.8027	-22.1767	3.1847	-12.4691
14	3.5395	0.0358	-0.1155	2.1584	1.7035	2.9024	-0.141	-0.0697	-0.2905	0.0378	0.0702	-0.3301	0.1833	0.3053	0.0538	0.1925	0.0261	-0.0141	0.1458	0.0341	0.3598	-18.0794	18.2861	3.2294
15	1.6893	0.5925	-0.2053	2.1101	0.3386	1.016	-0.0981	0.1202	-0.0437	-0.1244	0.1052	-0.1332	-0.0087	0.0942	-0.0022	0.1294	-0.0067	0.0148	0.1606	-0.0132	0.2641	-24.216	23.7251	-5.8485
16	1.6862	0.2242	0.567	1.6455	0.4966	1.3345	-0.012	-0.0171	0.1708	-0.0837	0.0146	0.5125	-0.1428	-0.0516	-0.0171	0.1329	-0.0171	0.0075	0.1729	-0.0084	0.3776	-40.6897	27.8898	-6.0915
17	4.5913	-0.4158	1.0735	1.4992	-1.0361	0.9346	0.0132	0.007	-0.2725	-0.1817	0.0694	0.2234	0.1163	-0.1245	-0.0648	0.161	-0.025	0.0069	0.1877	-0.016	0.3152	-44.2345	14.3067	-4.9021
18	0.5392	-0.0717	-0.6784	3.8106	1.0471	1.1854	-0.3878	0.433	-1.254	-0.1646	0.1947	-0.4623	0.1423	-0.0544	0.1446	0.2825	-0.0202	0.0342	0.3037	-0.079	0.4895	-39.6509	6.2246	27.9813
19	2.4313	0.3617	0.6911	2.9736	0.1943	1.2242	0.0406	-0.1096	-0.162	0.2672	-0.0421	-0.1687	-0.0056	0.0626	0.0111	0.2167	-0.0214	0.0219	0.2342	0.0016	0.2383	-31.9885	26.4271	35.6157
20	1.8752	-0.7203	1.6954	3.4502	-1.084	4.7357	0.0053	0.0775	0.2791	0.0712	0.0267	0.3553	-0.2527	-0.0779	-0.073	0.1832	-0.0123	0.0457	0.2617	-0.0027	0.3354	-49.338	31.7389	33.2032
21	5.5188	-0.2989	0.401	2.311	-0.6718	2.0882	-0.0443	-0.2204	0.1613	0.0987	0.0777	0.3109	-0.0389	-0.3206	-0.0382	0.1961	-0.0131	0.0391	0.2504	-0.0128	0.2174	-53.3073	18.166	33.8943

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 48 through 67 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 68 through 127 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 128 through 203 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 204 through 249 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 250 through 266 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 267 through 299 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 46 through 65 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 66 through 127 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 128 through 186 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 187 through 265 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 266 through 299 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 48 through 67 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 68 through 82 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 83 through 108 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 109 through 203 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 204 through 249 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 250 through 299 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 49 through 82 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 83 through 203 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 204 through 249 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 250 through 299 )

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Sample preparation

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-Non-polymers , 5 types, 617 molecules

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Protein , 1 types, 4 molecules ABCD

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