PDB-6e2h: Crystal structure of human Ash2L (SPRY domain and SDI motif) in c...

ID or keywords:

Entry

Database: PDB / ID: 6e2h

Title

Crystal structure of human Ash2L (SPRY domain and SDI motif) in complex with full length DPY-30

Components

Protein dpy-30 homolog
Set1/Ash2 histone methyltransferase complex subunit ASH2

Keywords

PROTEIN BINDING /

histone /

epigenetics /

SET1 / MLL / lysine methylation /

nucleosome

Function / homology

Function and homology information

MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / endosomal transport /

histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes /

MLL1 complex /

hemopoiesis / transcription initiation-coupled chromatin remodeling / Deactivation of the beta-catenin transactivating complex ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.236 Å

Authors

Joshi, M. / Brunzelle, J.S. / Couture, J.F.

Funding support

Canada, 1items

Citation

Journal: Structure / Year: 2018
Title: Structural Analysis of the Ash2L/Dpy-30 Complex Reveals a Heterogeneity in H3K4 Methylation.
Authors: Haddad, J.F. / Yang, Y. / Takahashi, Y.H. / Joshi, M. / Chaudhary, N. / Woodfin, A.R. / Benyoucef, A. / Yeung, S. / Brunzelle, J.S. / Skiniotis, G. / Brand, M. / Shilatifard, A. / Couture, J.F.

History

Deposition	Jul 11, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 8, 2018	Provider: repository / Type: Initial release
Revision 1.1	Oct 17, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Dec 19, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first / _citation_author.name
Revision 1.3	Jan 8, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Oct 11, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6e2h.cif.gz	146 KB	Display	PDBx/mmCIF format
PDB format	pdb6e2h.ent.gz	112.8 KB	Display	PDB format
PDBx/mmJSON format	6e2h.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/e2/6e2h ftp://data.pdbj.org/pub/pdb/validation_reports/e2/6e2h	HTTPS FTP

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Related structure data

Related structure data	4riqS S: Starting model for refinement
Similar structure data	1qfv-d 2yoy-d 3r0f-d 6nkc-d 3qzr-d 4x51-d 7a4d-2 4v0k-d 5ija-d 1zmr-d 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
Related items in Molecule of the Month	#7 - Jul 2000 Nucleosome similarity (2) #163 - Jul 2013 HIV Capsid similarity (6)

Deposited unit

D: Set1/Ash2 histone methyltransferase complex subunit ASH2

E: Protein dpy-30 homolog

F: Protein dpy-30 homolog

46.6 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

E: Protein dpy-30 homolog

F: Protein dpy-30 homolog

D: Set1/Ash2 histone methyltransferase complex subunit ASH2

defined by author&software
46.6 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	103.011, 103.011, 129.138
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

#1: Protein	Set1/Ash2 histone methyltransferase complex subunit ASH2 / ASH2-like protein Mass: 23974.178 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ASH2L, ASH2L1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UBL3
#2: Protein	Protein dpy-30 homolog / Dpy-30-like protein / Dpy-30L Mass: 11318.721 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DPY30 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9C005
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 188 / 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: 3.59 Å³/Da / Density % sol: 65.73 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion Details: 20mM citrate pH 4.7 and polyethylene glycol (PEG) 6000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 10, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.2→63.443 Å / Num. obs: 33958 / % possible obs: 99.4 % / Redundancy: 7.3 % / R_sym value: 0.043 / Net I/σ(I): 74.1
Reflection shell	Resolution: 2.2→2.31 Å / Num. unique obs: 402 / R_sym value: 0.043

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4RIQ

4riq

Resolution: 2.236→63.443 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.89 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1997	1747	5.14 %
R_work	0.1768	-	-
obs	0.178	33957	99.11 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.236→63.443 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2445	0	0	188	2633

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	2544
X-RAY DIFFRACTION	f_angle_d	0.679	3459
X-RAY DIFFRACTION	f_dihedral_angle_d	2.606	1897
X-RAY DIFFRACTION	f_chiral_restr	0.045	374
X-RAY DIFFRACTION	f_plane_restr	0.005	445

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 (%)
2.2357-2.3015	0.2863	133	0.2541	2441	X-RAY DIFFRACTION	92
2.3015-2.3758	0.2419	126	0.2276	2602	X-RAY DIFFRACTION	97
2.3758-2.4607	0.2121	137	0.2102	2671	X-RAY DIFFRACTION	100
2.4607-2.5593	0.2542	130	0.197	2678	X-RAY DIFFRACTION	100
2.5593-2.6757	0.2263	147	0.19	2656	X-RAY DIFFRACTION	100
2.6757-2.8168	0.2055	148	0.1895	2677	X-RAY DIFFRACTION	100
2.8168-2.9933	0.1984	141	0.1814	2707	X-RAY DIFFRACTION	100
2.9933-3.2244	0.2062	154	0.1773	2686	X-RAY DIFFRACTION	100
3.2244-3.5488	0.2169	170	0.1673	2686	X-RAY DIFFRACTION	100
3.5488-4.0623	0.1869	146	0.1534	2734	X-RAY DIFFRACTION	100
4.0623-5.1177	0.1475	160	0.1365	2753	X-RAY DIFFRACTION	100
5.1177-63.4689	0.2064	155	0.1987	2919	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	0.1077	0.0091	0.0364	0.0163	-0.0029	0.005	0.1421	0.3536	-0.1958	-0.1638	-0.1245	0.2362	0.1417	-0.0353	0.0002	0.3116	0.061	-0.0371	0.3591	-0.0331	0.3026	55.9751	86.967	-14.4442
2	0.0457	0.0506	-0.0058	0.0314	-0.0015	0.0329	0.1529	0.1768	0.1371	-0.0779	-0.0213	0.0528	-0.105	-0.2342	-0.0003	0.2244	0.075	0.068	0.267	0.0784	0.2675	54.5192	100.7489	-12.3452
3	0.0177	0.0216	0.0076	0.0196	0.0081	0.0224	0.2375	-0.0392	-0.1308	0.1332	-0.0739	0.0475	0.167	-0.1466	-0	0.3429	0.0051	-0.0396	0.2126	0.022	0.3176	60.9469	85.3054	-4.1634
4	0.1001	0.0135	-0.0493	0.0308	0.1157	0.4008	0.2093	-0.011	0.0678	-0.0253	-0.118	-0.0316	-0.0493	-0.0124	0	0.2239	0.0031	0.0492	0.1966	0.0285	0.2747	58.4255	99.3374	-3.0832
5	0.1823	-0.1784	0.0933	0.1164	-0.0251	0.1997	0.1	-0.097	0.2459	0.0605	0.0305	0.0846	-0.053	-0.0479	0.0002	0.2546	-0.0568	0.0447	0.2366	-0.0068	0.3006	58.9486	101.4379	5.5804
6	0.0261	-0.0145	-0.0242	0.0225	-0.0333	0.0081	0.0257	0.0052	0.0457	-0.072	0.1092	-0.0788	0.2242	0.1741	0.0002	0.2868	0.0398	-0.039	0.2087	0.0264	0.2946	68.0443	85.2002	7.0129
7	0.2697	-0.1234	-0.0271	0.1784	0.2884	0.3985	0.1061	-0.0202	0.0623	0.0004	-0.0301	-0.0937	0.0576	0.1105	0	0.2484	-0.0067	0.0252	0.2471	0.0285	0.2561	64.6869	96.1155	-0.6473
8	-0.0047	-0.0502	0.0127	0.0304	0.025	-0.0256	-0.043	-0.0615	0.0741	-0.0982	0.0176	-0.0857	-0.0601	0.0711	0	0.271	0.0453	0.0065	0.2809	0.0133	0.2285	78.6893	79.7978	-12.2023
9	0.0182	-0.0163	0.0157	0.0081	-0.0071	0.0064	-0.0722	0.1511	0.0146	0.0041	0.0615	-0.3503	0.0793	0.0676	0.0003	0.3644	-0.0321	0.0376	0.5181	-0.2592	0.6889	28.4499	65.6672	6.863
10	0.593	0.1432	0.4778	0.0768	0.1156	0.4372	-0.4727	0.9099	0.2707	-0.2411	0.154	-0.0256	-0.1829	0.4893	-0.126	0.3822	-0.292	0.0223	0.4942	0.0548	0.2566	26.1469	83.6017	6.1366
11	0.0746	0.0359	0.1274	0.0928	0.0474	0.2611	-0.0357	0.0238	-0.0203	-0.1027	0.031	0.0589	-0.0129	-0.1496	-0.0795	0.7162	-0.2087	-0.2545	0.5666	0.2587	0.4173	15.7327	88.0193	1.6327
12	0.1035	0.0294	0.0167	0.0112	0.0309	0.1415	-0.0836	-0.048	-0.0221	-0.2464	-0.0482	-0.0746	-0.0063	0.0993	-0.1038	0.6339	-0.5039	0.1421	0.9658	0.2033	0.183	27.3212	81.5545	-3.4007
13	0.1049	-0.0215	0.0306	0.1306	-0.0147	0.0255	-0.3005	0.2926	0.2102	0.0716	0.3156	0.4062	0.0233	-0.1268	0.0062	0.2974	-0.0898	-0.0418	0.3561	0.0602	0.3735	16.314	83.9264	12.293
14	0.0114	-0.0178	0.0078	0.0674	0.0195	0.0342	-0.0434	0.0852	-0.1534	-0.1443	0.0313	-0.0147	0.0011	-0.0197	0.0149	0.3202	-0.4705	-0.0719	0.3545	-0.3504	0.2282	20.7226	65.5193	0.5863
15	0.0817	0.1539	-0.0987	0.5959	-0.3307	0.1908	0.0183	0.0583	0.0326	-0.2003	-0.0342	-0.0446	0.0128	0.0715	-0.0662	1.0289	-0.4511	0.1276	0.9193	-0.2278	0.022	23.4963	72.6257	-4.3373
16	0.0889	-0.0134	0.0215	0.0309	-0.0189	0.0142	-0.2172	0.1525	0.0457	-0.4293	-0.0867	0.4261	0.0218	0.0625	-0.0012	0.4886	-0.2034	-0.1167	0.5924	0.0361	0.4541	12.2474	77.6983	0.2998

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain D and resid 278:297)
2	X-RAY DIFFRACTION	2	(chain D and resid 298:315)
3	X-RAY DIFFRACTION	3	(chain D and resid 316:326)
4	X-RAY DIFFRACTION	4	(chain D and resid 327:357)
5	X-RAY DIFFRACTION	5	(chain D and resid 358:391)
6	X-RAY DIFFRACTION	6	(chain D and resid 392:409)
7	X-RAY DIFFRACTION	7	(chain D and resid 410:454)
8	X-RAY DIFFRACTION	8	(chain D and resid 455:491)
9	X-RAY DIFFRACTION	9	(chain E and resid 50:58)
10	X-RAY DIFFRACTION	10	(chain E and resid 59:77)
11	X-RAY DIFFRACTION	11	(chain E and resid 78:83)
12	X-RAY DIFFRACTION	12	(chain E and resid 84:96)
13	X-RAY DIFFRACTION	13	(chain F and resid 47:69)
14	X-RAY DIFFRACTION	14	(chain F and resid 70:78)
15	X-RAY DIFFRACTION	15	(chain F and resid 79:83)
16	X-RAY DIFFRACTION	16	(chain F and resid 84:96)

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