PDB-5ht6: Crystal structure of the SET domain of the human MLL5 methyltrans...

ID or keywords:

Entry

Database: PDB / ID: 5ht6

Title

Crystal structure of the SET domain of the human MLL5 methyltransferase

Components

Histone-lysine N-methyltransferase 2E

Keywords

TRANSFERASE /

SET domain

Function / homology

Function and homology information

Set3 complex / Rpd3L-Expanded complex /

neutrophil activation / neutrophil mediated immunity / : / positive regulation of G1/S transition of mitotic cell cycle / methylated histone binding /

erythrocyte differentiation /

euchromatin / chromatin organization ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.093 Å

Authors

le Maire, A. / Mas-y-Mas, S. / Dumas, C. / Lebedev, A.

Funding support

France, 1items

Citation

Journal: Plos One / Year: 2016
Title: The Human Mixed Lineage Leukemia 5 (MLL5), a Sequentially and Structurally Divergent SET Domain-Containing Protein with No Intrinsic Catalytic Activity.
Authors: Mas-Y-Mas, S. / Barbon, M. / Teyssier, C. / Demene, H. / Carvalho, J.E. / Bird, L.E. / Lebedev, A. / Fattori, J. / Schubert, M. / Dumas, C. / Bourguet, W. / le Maire, A.

History

Deposition	Jan 26, 2016	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Nov 16, 2016	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5ht6.cif.gz	114.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5ht6.ent.gz	90.5 KB	Display	PDB format
PDBx/mmJSON format	5ht6.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/ht/5ht6 ftp://data.pdbj.org/pub/pdb/validation_reports/ht/5ht6	HTTPS FTP

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Related structure data

Similar structure data	4drz-d 1ijx-3 1yzt-1 3dxc-2 5xga-d 6xcg-2 4qn8-2 5ybd-2 6nni-1 1unq-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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 2E

B: Histone-lysine N-methyltransferase 2E

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

1

A: Histone-lysine N-methyltransferase 2E

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

2

B: Histone-lysine N-methyltransferase 2E

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

Unit cell

Length a, b, c (Å)	65.900, 65.900, 112.900
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	Histone-lysine N-methyltransferase 2E / Lysine N-methyltransferase 2E / Myeloid/lymphoid or mixed-lineage leukemia protein 5 Mass: 16107.490 Da / Num. of mol.: 2 / Fragment: UNP residues 323-458 / Mutation: C453A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KMT2E, MLL5 / Production host: Escherichia coli (E. coli) References: UniProt: Q8IZD2, histone-lysine N-methyltransferase
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Histone-lysine N-methyltransferase 2E / Lysine N-methyltransferase 2E / Myeloid/lymphoid or mixed-lineage leukemia protein 5

Mass: 16107.490 Da / Num. of mol.: 2 / Fragment: UNP residues 323-458 / Mutation: C453A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: KMT2E, MLL5 / Production host:

Escherichia coli (E. coli)
References: UniProt: Q8IZD2,

histone-lysine N-methyltransferase

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.2 Å³/Da / Density % sol: 44.01 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M NH4Cl, 12 % (w/v) PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07245 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.07245 Å / Relative weight: 1
Reflection	Resolution: 2.093→57.174 Å / Num. obs: 17289 / % possible obs: 99.9 % / Redundancy: 8 % / R_sym value: 0.057 / Net I/σ(I): 22
Reflection shell	Resolution: 2.1→2.21 Å / Redundancy: 8.4 % / R_merge(I) obs: 0.39 / Mean I/σ(I) obs: 2 / R_sym value: 0.39 / % possible all: 99.7

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
SCALA	3.3.21	data scaling
PDB_EXTRACT	3.15	data extraction
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.093→50.933 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.12 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2424	1306	7.57 %
R_work	0.2089	-	-
obs	0.2116	17250	99.53 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.093→50.933 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1928	0	0	80	2008

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	1988
X-RAY DIFFRACTION	f_angle_d	0.841	2676
X-RAY DIFFRACTION	f_dihedral_angle_d	13.084	747
X-RAY DIFFRACTION	f_chiral_restr	0.031	274
X-RAY DIFFRACTION	f_plane_restr	0.005	343

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 (%)
2.0928-2.1766	0.3435	145	0.2667	1705	X-RAY DIFFRACTION	97
2.1766-2.2757	0.2775	118	0.2526	1747	X-RAY DIFFRACTION	100
2.2757-2.3957	0.3561	127	0.2517	1770	X-RAY DIFFRACTION	100
2.3957-2.5458	0.3242	144	0.2391	1742	X-RAY DIFFRACTION	100
2.5458-2.7423	0.275	132	0.229	1784	X-RAY DIFFRACTION	100
2.7423-3.0183	0.2603	137	0.2269	1766	X-RAY DIFFRACTION	100
3.0183-3.4549	0.252	186	0.2149	1748	X-RAY DIFFRACTION	100
3.4549-4.3525	0.2066	159	0.1788	1797	X-RAY DIFFRACTION	100
4.3525-50.9484	0.208	158	0.1901	1885	X-RAY DIFFRACTION	100

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	3.7391	-0.7673	2.2312	2.7249	-1.2043	7.1879	-0.7875	-0.5659	-1.3779	0.9614	0.4498	0.8801	0.7013	-1.9588	0.1054	0.8227	-0.2079	0.1985	0.8808	0.1936	0.819	17.3238	-20.0689	30.2266
2	3.5346	-2.1313	-1.174	1.2806	0.6808	0.9555	-0.518	-0.4133	-0.663	0.396	-0.1062	0.2421	0.7879	0.0628	-0.063	0.9847	0.3919	0.4761	-0.0367	0.0335	0.6846	30.9049	-23.1149	26.2121
3	8.7971	-5.9643	-0.8416	4.5517	-1.0221	5.1143	0.0193	0.4956	-0.8698	-0.3321	-0.0584	1.1215	0.9758	-0.4571	0.013	0.4692	-0.1666	0.0334	0.2686	-0.0842	0.5106	20.1654	-14.5878	19.1111
4	4.3161	-3.3756	-2.5418	6.6713	1.0112	8.8797	0.5955	1.2249	0.1454	-0.4971	-0.7106	0.6796	-0.8978	-1.4219	0.0857	0.3013	0.1257	0.0197	0.5317	0.0661	0.5631	15.2659	3.1225	15.7706
5	3.8815	-0.5002	-0.2214	4.7887	-3.0361	6.5855	-0.2404	0.0542	0.3014	0.7951	0.2014	0.9254	-0.7421	-1.7778	0.0154	0.4189	0.1294	0.1465	0.6202	-0.0396	0.4086	13.6906	2.5154	25.0091
6	3.3312	-0.4929	-1.5529	4.3205	-0.3836	7.162	0.2778	-0.2685	0.3531	0.0857	-0.0888	0.2517	-0.2228	0.1036	-0.0922	0.1592	-0.0417	0.0187	0.2718	0.0019	0.3324	25.1905	-0.7324	18.0104
7	2.2506	1.4209	0.0354	7.6825	-0.55	4.1996	-0.2611	-0.3446	-0.3073	-0.0463	-0.3375	1.4393	0.2538	-2.0115	0.0815	0.2628	-0.1781	0.0815	0.7625	-0.0779	0.7614	13.0905	-7.0014	19.0781
8	5.9337	-0.9866	1.5697	3.9068	0.3299	6.1965	-0.3363	-0.2225	-0.1803	0.537	0.1717	0.5859	1.143	-0.4788	0.1334	0.4834	-0.0358	0.1288	0.3183	0.0753	0.3272	21.5549	-11.0593	30.5149
9	4.148	-1.114	-1.8748	5.418	-1.2639	1.4596	-0.1524	0.4634	-0.7204	-0.1612	-0.0805	0.2426	1.231	0.308	0.1037	0.329	0.0211	-0.0138	0.2226	-0.0386	0.2845	27.9787	-10.6181	15.9923
10	4.6884	-1.2827	0.3492	5.511	-2.1877	4.5328	-0.1993	-0.0206	-0.5791	0.3102	0.3172	0.4769	1.2262	0.1389	-0.1688	0.5608	0.0896	0.0235	0.2097	-0.0359	0.2873	26.4368	-15.5311	22.672
11	0.8488	-1.1083	-1.2649	7.8398	5.416	4.1854	-0.3793	-0.0924	0.155	0.5107	0.7178	-0.016	-0.3407	0.1699	-0.2875	0.4378	-0.0139	0.0069	0.3098	0.0078	0.3217	23.9634	-1.0651	31.5384
12	7.9127	-1.1776	1.252	7.1775	0.7738	2.0482	0.4971	0.5148	-0.8975	-0.0714	0.1797	-0.3397	0.117	0.9275	-0.7674	0.6013	-0.1861	-0.1437	0.5403	0.0028	0.4944	32.0516	8.2523	32.8661
13	6.5308	1.7066	1.3663	6.33	-2.2008	5.5089	-0.5047	0.5408	0.0896	-0.186	0.4528	0.4827	0.2121	-0.3902	0.0406	0.845	0.1379	0.142	0.4594	0.0834	0.4143	27.5121	21.9138	-8.3893
14	4.6847	4.3386	-1.0335	5.6509	-3.512	4.274	0.3001	-0.6021	0.3018	0.0091	0.4887	1.2258	-0.8335	-0.5775	-0.3726	0.6655	0.3174	0.1626	0.3706	0.1756	0.5094	23.1521	15.8856	1.4821
15	5.7931	1.0847	0.3817	2.1466	-3.174	7.6509	0.6151	-0.3678	-0.8454	-0.6837	0.7755	0.9805	1.2373	-1.9954	-0.9618	0.5563	-0.0728	-0.2502	0.8354	0.1944	0.9803	14.7905	0.0459	5.084
16	0.3115	0.3459	0.0575	3.196	-2.7728	3.5883	0.2225	0.2946	0.2185	-0.8567	-0.3315	1.0485	0.1982	-1.4776	0.0204	0.9768	-0.0667	-0.3883	1.3861	0.2229	1.0471	12.0838	0.8139	-3.3788
17	4.4627	-1.8454	0.0564	7.5988	-3.872	5.8431	0.0973	0.4608	-0.0268	-1.7431	0.0556	0.274	0.8595	-0.6488	-0.1427	0.4964	0.0601	-0.0509	0.3877	0.0525	0.3491	24.5698	1.2947	1.7002
18	1.7622	-0.875	0.4854	3.772	-2.4121	1.5356	0.0123	-0.2616	0.0118	-0.6002	0.0324	0.5777	-0.7148	-1.3102	-0.3303	0.7111	0.5468	-0.1901	1.035	0.2921	0.6193	14.9027	12.2847	0.2201
19	2.1419	1.2413	-0.1533	2.6521	-3.1234	4.9878	0.1092	0.3346	0.3383	-1.2705	-0.0409	0.2196	-0.3181	-0.6837	-0.1234	1.1253	0.1249	0.1273	0.3751	0.1071	0.3884	27.429	10.6237	-4.4633
20	1.35	1.3014	-0.6128	5.0437	-3.6554	2.7257	0.3238	0.0066	0.2499	-0.1416	0.3159	0.2157	-1.0075	-0.5375	-0.3529	0.7992	0.1881	0.1785	0.2187	0.0511	0.3335	28.895	15.8622	-2.7744
21	5.9009	-3.5503	2.3695	2.9439	-0.5897	1.816	0.7374	0.4118	-1.4263	-1.5874	0.4451	0.6471	1.8525	-1.1271	-0.9716	1.9022	-0.0202	-0.2201	0.6789	0.0317	0.5921	23.9455	5.1834	-10.3361

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 24 through 42 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 43 through 50 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 51 through 57 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 58 through 67 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 68 through 78 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 79 through 89 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 90 through 99 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 100 through 111 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 112 through 119 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 120 through 139 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 140 through 149 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 150 through 154 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 37 through 50 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 51 through 57 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 58 through 66 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 67 through 78 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 79 through 89 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 90 through 103 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 104 through 119 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 120 through 139 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 140 through 145 )

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