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

ID or keywords:

Entry

Database: PDB / ID: 37eu

Title

Crystal Structure of Histone-lysine N-methyltransferase from Leishmania major in complex with S-ADENOSYL-L-HOMOCYSTEINE (P21 form)

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: 2.1 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-ADENOSYL-L-HOMOCYSTEINE (P21 form)
Authors: Liu, L. / Lovell, S. / Battaile, K.P.

History

Deposition	Jul 17, 2026	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 29, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	37eu.cif.gz	424 KB	Display	PDBx/mmCIF format
PDB format	pdb37eu.ent.gz	347.8 KB	Display	PDB format
PDBx/mmJSON format	37eu.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/7e/37eu ftp://data.pdbj.org/pub/pdb/validation_reports/7e/37eu	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

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
30.4 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
30.3 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
30.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	69.949, 91.846, 82.265
Angle α, β, γ (deg.)	90.00, 102.96, 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 , 7 types, 601 molecules

#2: Chemical	ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 583 / 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: 2.17 Å³/Da / Density % sol: 43.39 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 25% P3350, Bis-Tris 5.5, 0.2M NaCl. LemaA.18205.a.B2.PW39520 at 12.4 mg/mL. BTB bound from crystallant and SAH from the expression host , plate 20826 G7, Puck: PSL-1805, Cryo: 33% P3350, Bis-Tris 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: Feb 25, 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: 2.1→46.99 Å / Num. obs: 59204 / % possible obs: 99.9 % / Redundancy: 7 % / CC_1/2: 0.995 / R_merge(I) obs: 0.198 / R_pim(I) all: 0.081 / R_rim(I) all: 0.214 / Χ²: 1.09 / Net I/σ(I): 7.9 / Num. measured all: 412872
Reflection shell	Resolution: 2.1→2.15 Å / % possible obs: 100 % / Redundancy: 6.8 % / R_merge(I) obs: 0.867 / Num. measured all: 29747 / Num. unique obs: 4355 / CC_1/2: 0.864 / R_pim(I) all: 0.356 / R_rim(I) all: 0.938 / Χ²: 1.02 / Net I/σ(I) obs: 2.3

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Processing

Software

Name	Version	Classification
PHENIX	2.0_5936	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.1→46.99 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.63 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2694	2909	4.93 %
R_work	0.2437	-	-
obs	0.245	59052	99.69 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.1→46.99 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8031	0	175	583	8789

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	8489
X-RAY DIFFRACTION	f_angle_d	0.659	11525
X-RAY DIFFRACTION	f_dihedral_angle_d	12.005	3142
X-RAY DIFFRACTION	f_chiral_restr	0.044	1256
X-RAY DIFFRACTION	f_plane_restr	0.006	1470

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 (%)
2.1-2.13	0.3217	144	0.2945	2682	X-RAY DIFFRACTION	100
2.13-2.17	0.2994	131	0.2915	2645	X-RAY DIFFRACTION	100
2.17-2.21	0.33	156	0.2822	2658	X-RAY DIFFRACTION	100
2.21-2.25	0.3022	123	0.2799	2659	X-RAY DIFFRACTION	100
2.25-2.3	0.2598	135	0.2644	2678	X-RAY DIFFRACTION	100
2.3-2.35	0.299	126	0.2674	2663	X-RAY DIFFRACTION	100
2.35-2.4	0.2767	126	0.2755	2681	X-RAY DIFFRACTION	100
2.4-2.46	0.3072	138	0.258	2669	X-RAY DIFFRACTION	100
2.46-2.53	0.2982	133	0.2584	2649	X-RAY DIFFRACTION	100
2.53-2.61	0.2773	145	0.2512	2679	X-RAY DIFFRACTION	100
2.61-2.69	0.3059	152	0.2654	2673	X-RAY DIFFRACTION	100
2.69-2.79	0.2791	156	0.2468	2619	X-RAY DIFFRACTION	100
2.79-2.9	0.3169	111	0.2579	2718	X-RAY DIFFRACTION	100
2.9-3.03	0.2966	147	0.2518	2659	X-RAY DIFFRACTION	100
3.03-3.19	0.2979	144	0.2581	2678	X-RAY DIFFRACTION	100
3.19-3.39	0.2526	140	0.2426	2665	X-RAY DIFFRACTION	100
3.39-3.65	0.2434	130	0.2203	2670	X-RAY DIFFRACTION	99
3.65-4.02	0.2307	119	0.2134	2703	X-RAY DIFFRACTION	100
4.02-4.6	0.2517	150	0.2026	2695	X-RAY DIFFRACTION	100
4.6-5.79	0.207	159	0.2146	2670	X-RAY DIFFRACTION	100
5.79-46.99	0.2467	144	0.2406	2730	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	0.0686	0.0319	-0.2453	0.0298	-0.1488	0.9844	-0.053	0.2448	-0.0515	-0.2967	0.1089	-0.1383	0.1512	-0.2485	0.0096	0.1508	-0.0048	0.0122	0.114	-0.0517	0.3513	-11.6358	-18.6702	29.462
2	0.0464	-0.0318	0.0483	0.1195	0.0136	0.0251	-0.0137	0.1102	-0.0886	0.0181	0.3359	-0.0476	0.0508	-0.0221	0.3212	0.1567	0.0271	0.0646	0.0961	-0.2002	0.5909	3.5283	-16.9077	28.0135
3	0.1118	0.0918	0.0871	0.1801	-0.0353	0.2163	0.0385	-0.1981	-0.5476	0.1558	-0.0707	-0.273	-0.0407	0.0408	-0.0491	0.1555	0.0192	-0.0102	0.136	-0.0127	0.3278	7.6996	-2.0012	43.3966
4	0.0256	0.0377	0.0533	0.2573	0.0268	0.1881	-0.0558	0.0888	-0.1448	-0.0368	-0.0088	0.091	-0.0204	0.0019	-0.0329	0.094	-0.0084	0.026	0.0769	-0.0171	0.1549	-2.6244	0.54	33.74
5	0.2522	-0.3371	0.2059	0.7811	-0.3839	0.5761	-0.1005	0.0282	-0.1997	0.1959	0.0293	-0.025	-0.1574	0.0664	0.0455	0.0964	-0.0196	-0.027	0.0814	-0.0227	0.2793	10.7488	5.3365	35.9834
6	0.1553	0.2723	0.1847	0.6431	-0.1238	0.2283	-0.0022	0.0179	0.2908	-0.1765	0.1055	0.5097	-0.0999	0.0123	0.0333	0.0228	-0.0143	0.0671	0.0937	0.0016	0.1489	-14.2173	5.9347	34.4649
7	0.2891	0.0989	-0.094	0.1454	-0.0105	0.2467	-0.0513	0.1563	-0.2183	-0.2684	0.0213	-0.0494	0.072	-0.0361	-0.0444	0.0787	0.002	0.0005	0.1231	0.0263	0.209	-14.4794	-7.3795	34.4811
8	0.0154	0.0617	-0.0113	0.1969	-0.0177	0.1911	-0.0088	0.1251	-0.1614	-0.2008	0.2355	-0.1031	0.1915	-0.2173	0.2449	0.3369	0.0696	0.0056	0.326	-0.2762	-0.208	-21.0565	-14.4571	68.4328
9	0.0071	0.0027	0.0051	0.0026	-0.0098	0.0178	-0.1602	0.0981	-0.0472	0.085	0.4711	-0.1812	-0.0719	-0.1347	0	0.3784	0.0072	0.0369	0.412	-0.1201	0.3728	-5.3774	-13.1189	67.3979
10	0.2369	0.1579	-0.0568	0.1668	-0.1597	0.1182	0.0747	-0.033	0.0278	0.1142	-0.1238	-0.0006	0.1469	-0.1414	0	0.3413	-0.0199	-0.0111	0.3456	-0.034	0.1802	-8.4239	2.2706	77.5821
11	0.2554	0.2349	0.0842	0.2763	0.0957	0.0716	0.0978	-0.0898	-0.2955	0.3639	-0.2339	-0.4218	-0.116	0.0202	-0.076	0.35	-0.067	0.0143	0.4048	-0.0049	0.0541	-2.8764	8.3869	74.292
12	0.5211	0.5776	-0.0115	0.6644	-0.0739	0.0305	0.0573	0.2181	0.2697	-0.1006	-0.0551	0.3157	0.0607	-0.0682	-0.016	0.3992	-0.0165	0.0248	0.357	0.031	0.1769	-15.9071	13.2426	72.9374
13	0.0714	0.0219	-0.0077	0.0401	-0.0137	-0.0109	0.029	0.0029	0.485	-0.0826	0.003	0.5713	0.2173	-0.2026	0.0013	0.33	-0.05	-0.0039	0.4137	0.0049	0.3334	-27.0395	10.122	74.2333
14	0.0932	0.0861	-0.0012	0.0662	-0.0079	-0.0054	0.0898	-0.0511	0.0088	0.1867	0.1133	0.096	0.1345	-0.4715	0.0099	0.3235	0.0288	0.0614	0.5428	0.0457	0.222	-36.3636	0.7806	75.4999
15	0.3512	0.3678	0.1794	0.3794	0.1874	0.1169	-0.0941	0.0718	0.2213	-0.1648	-0.1417	0.2579	-0.0829	-0.0959	-0.02	0.4093	0.0593	-0.0054	0.554	-0.0393	0.1164	-29.3635	-0.898	69.8593
16	0.0606	0.0278	0.0546	0.0257	0.0481	0.0523	-0.057	-0.0903	-0.0088	-0.0155	0.0442	0.0862	0.0825	-0.0666	-0.1108	0.298	-0.0172	-0.0151	0.3172	0.0091	0.0813	-20.094	-5.3524	76.0146
17	0.0079	-0.0079	0.0136	0.1038	-0.1629	0.3227	0.062	-0.0887	0.0651	0.2861	0.0453	0.1283	-0.3063	-0.0693	0.0241	0.189	-0.017	0.0417	0.1666	-0.0467	0.3348	-46.7444	-1.5974	51.0421
18	0.0259	0.0015	-0.0213	0.0083	-0.004	0.0364	-0.2488	-0.1646	0.1532	0.0756	0.2591	-0.0698	-0.0765	-0.044	0.0022	0.2106	0.0336	-0.0154	0.1873	-0.0935	0.4051	-31.1631	-3.0727	52.8351
19	0.229	-0.2355	0.0419	0.2013	-0.0684	0.2306	0.0038	0.0269	0.2332	-0.0853	-0.024	0.1294	-0.1874	-0.0587	-0.0272	0.0986	-0.0075	-0.0322	0.0863	-0.002	0.2151	-32.1051	-16.9569	39.532
20	0.312	-0.5073	-0.1318	0.8831	-0.0375	0.567	-0.0233	0.0094	-0.0744	0.0084	0.0696	0.2643	0.0564	-0.0036	0.1124	0.0791	0.0104	-0.0312	0.074	0.0012	0.2099	-38.8825	-26.6832	47
21	0.0143	-0.0132	0.0034	0.0025	-0.0096	0.0462	0.0285	-0.0006	-0.0618	0.0728	0.133	0.2906	-0.1637	-0.1189	0.2538	0.0083	0.005	-0.0603	0.1474	0.095	0.5518	-62.1372	-17.3981	44.5679
22	0.2625	0.1474	0.2442	0.1727	0.0515	0.2993	-0.1882	-0.015	-0.2951	0.0865	0.0663	0.1833	0.1272	0.0273	-0.0395	0.098	0.0146	0.0175	0.1014	0.042	0.3106	-49.6095	-12.9427	46.5277
23	-0.0039	0.0133	-0.0067	0.0397	-0.0264	0.0064	-0.2272	-0.2314	0.0602	0.3696	0.203	-0.0352	-0.0976	-0.1349	0	0.3375	-0.0157	0.0162	0.4227	-0.0092	0.2821	-55.6123	2.2114	90.8186
24	0.1304	-0.1485	0.0329	0.3069	-0.2039	0.1115	-0.0471	-0.06	-0.0545	-0.1493	0.0433	0.0977	-0.0865	-0.0883	0.0001	0.3285	0.0053	-0.0339	0.3016	-0.0618	0.1561	-41.5787	-10.0953	82.0837
25	0.4979	-0.4283	0.1945	0.6261	0.0243	-0.0001	0.0347	-0.1857	-0.3172	-0.1956	0.0317	0.1707	0.0108	0.0258	0.0102	0.3066	-0.0144	-0.0271	0.3308	0.0223	0.2167	-47.8307	-22.9388	86.5737
26	0.1468	-0.04	-0.0422	0.7788	-0.2876	0.1174	0.1897	0.1071	-0.2487	-0.0563	0.0959	0.2243	0.128	-0.0306	0.1349	0.3685	-0.0137	-0.0872	0.3499	-0.0094	0.1228	-71.0566	-13.7134	83.5905
27	0.1699	-0.1536	0.0827	0.122	0.0525	0.1527	-0.1781	-0.1746	-0.0109	-0.2179	-0.0842	0.0975	0.1642	-0.1645	0	0.2914	-0.0204	-0.0411	0.392	-0.0098	0.2359	-59.056	-9.3733	85.6474

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 82 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 83 through 108 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 109 through 164 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 165 through 186 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 187 through 266 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 267 through 299 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 48 through 67 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 68 through 82 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 83 through 144 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 145 through 186 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 187 through 227 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 228 through 249 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 250 through 266 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 267 through 279 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 280 through 299 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 48 through 67 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 68 through 82 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 83 through 127 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 128 through 249 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 250 through 266 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 267 through 299 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 48 through 67 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 68 through 128 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 129 through 249 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 250 through 265 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 266 through 299 )

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