PDB-3toj: Structure of the SPRY domain of human Ash2L

ID or keywords:

Entry

Database: PDB / ID: 3toj

Title

Structure of the SPRY domain of human Ash2L

Components

Set1/Ash2 histone methyltransferase complex subunit ASH2

Keywords

TRANSCRIPTION /

histone methyltransferase / SPRY domain /

protein binding /

histone methylation /

RbBP5 / DPY-30 / nuclear

Function / homology

Function and homology information

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

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 / Formation of the beta-catenin:TCF transactivating complex ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.07 Å

Authors

Chen, Y. / Cao, F. / Wan, B. / Dou, Y. / Lei, M.

Citation

Journal: Cell Res. / Year: 2012
Title: Structure of the SPRY domain of human Ash2L and its interactions with RbBP5 and DPY30.
Authors: Chen, Y. / Cao, F. / Wan, B. / Dou, Y. / Lei, M.

History

Deposition	Sep 5, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 25, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jul 18, 2012	Group: Database references
Revision 1.2	Aug 23, 2017	Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3toj.cif.gz	171.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3toj.ent.gz	143.6 KB	Display	PDB format
PDBx/mmJSON format	3toj.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/to/3toj ftp://data.pdbj.org/pub/pdb/validation_reports/to/3toj	HTTPS FTP

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Related structure data

Similar structure data	1pt6-d 5oea-4 5cuz-1 2ouh-d 6dd1-d 1rd7-d 2ynw-d 5oee-1 6th2-2 6hkw-4 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	#163 - Jul 2013 HIV Capsid similarity (6)

Deposited unit

A: Set1/Ash2 histone methyltransferase complex subunit ASH2

B: Set1/Ash2 histone methyltransferase complex subunit ASH2

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	115.289, 115.289, 105.780
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	Set1/Ash2 histone methyltransferase complex subunit ASH2 / ASH2-like protein Mass: 23935.055 Da / Num. of mol.: 2 / Fragment: Ash2L SPRY domain, UNP residues 370-496, 539-617 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: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Set1/Ash2 histone methyltransferase complex subunit ASH2 / ASH2-like protein

Mass: 23935.055 Da / Num. of mol.: 2 / Fragment: Ash2L SPRY domain, UNP residues 370-496, 539-617
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: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal	Density Matthews: 4.24 Å³/Da / Density % sol: 70.99 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20% PEG4000, 0.15 M Li2SO4, 0.1 M Tris, pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 25, 2009
Radiation	Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9787 Å / Relative weight: 1
Reflection	Resolution: 2.07→100 Å / Num. all: 49302 / Num. obs: 49204 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell	Resolution: 2.07→2.11 Å / % possible all: 99

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
SHARP		phasing
PHENIX	(phenix.refine: 1.7_650)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.07→36.304 Å / SU ML: 0.25 / σ(F): 1.35 / Phase error: 19.28 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2061	4926	10.02 %	10% of dataset
R_work	0.1756	-	-	-
obs	0.1786	49163	98.23 %	-
all	-	49204	-	-

Solvent computation

Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 60.294 Å² / k_sol: 0.375 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.5955 Å²	0 Å²	0 Å²
2-	-	-2.5955 Å²	-0 Å²
3-	-	-	5.191 Å²

Refinement step

Cycle: LAST / Resolution: 2.07→36.304 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3115	0	0	271	3386

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	3228
X-RAY DIFFRACTION	f_angle_d	1.016	4371
X-RAY DIFFRACTION	f_dihedral_angle_d	12.647	1173
X-RAY DIFFRACTION	f_chiral_restr	0.079	441
X-RAY DIFFRACTION	f_plane_restr	0.005	562

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 (%)
2.07-2.091	0.247	48	0.2262	835	X-RAY DIFFRACTION	52
2.091-2.1156	0.259	149	0.2014	1468	X-RAY DIFFRACTION	99
2.1156-2.1414	0.2245	152	0.1856	1492	X-RAY DIFFRACTION	100
2.1414-2.1685	0.211	167	0.1706	1499	X-RAY DIFFRACTION	100
2.1685-2.197	0.1976	177	0.1591	1439	X-RAY DIFFRACTION	100
2.197-2.2271	0.2094	179	0.1652	1474	X-RAY DIFFRACTION	100
2.2271-2.2589	0.2196	160	0.1702	1494	X-RAY DIFFRACTION	100
2.2589-2.2927	0.2151	162	0.1705	1482	X-RAY DIFFRACTION	100
2.2927-2.3285	0.1973	183	0.172	1462	X-RAY DIFFRACTION	100
2.3285-2.3666	0.2314	160	0.1752	1487	X-RAY DIFFRACTION	100
2.3666-2.4074	0.2279	172	0.1775	1498	X-RAY DIFFRACTION	100
2.4074-2.4512	0.2003	169	0.171	1475	X-RAY DIFFRACTION	100
2.4512-2.4983	0.2158	166	0.1716	1463	X-RAY DIFFRACTION	100
2.4983-2.5493	0.2094	157	0.1739	1491	X-RAY DIFFRACTION	100
2.5493-2.6047	0.2115	186	0.1873	1489	X-RAY DIFFRACTION	100
2.6047-2.6653	0.2538	186	0.1842	1472	X-RAY DIFFRACTION	100
2.6653-2.732	0.2317	184	0.1867	1466	X-RAY DIFFRACTION	100
2.732-2.8058	0.2182	156	0.1853	1523	X-RAY DIFFRACTION	100
2.8058-2.8883	0.2114	170	0.1844	1481	X-RAY DIFFRACTION	100
2.8883-2.9815	0.2234	171	0.1863	1484	X-RAY DIFFRACTION	100
2.9815-3.088	0.2165	167	0.1864	1497	X-RAY DIFFRACTION	100
3.088-3.2116	0.2388	150	0.1827	1534	X-RAY DIFFRACTION	100
3.2116-3.3577	0.1934	177	0.1853	1481	X-RAY DIFFRACTION	100
3.3577-3.5345	0.227	163	0.1748	1526	X-RAY DIFFRACTION	100
3.5345-3.7558	0.18	154	0.1779	1518	X-RAY DIFFRACTION	100
3.7558-4.0454	0.2045	174	0.1623	1514	X-RAY DIFFRACTION	100
4.0454-4.4519	0.1658	179	0.1439	1517	X-RAY DIFFRACTION	100
4.4519-5.0945	0.169	169	0.1374	1523	X-RAY DIFFRACTION	100
5.0945-6.4128	0.1929	178	0.1828	1540	X-RAY DIFFRACTION	100
6.4128-36.3095	0.2363	161	0.222	1613	X-RAY DIFFRACTION	98

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	0.2317	-0.0013	0.2191	0.4048	0.3035	0.3779	-0.0018	-0.0207	0.1015	0.1123	-0.0088	-0.1823	0.0021	0.0921	0.0089	0.3404	0.0589	0.0856	0.1688	0.0047	0.2308	4.5863	93.1698	19.6869
2	0.4677	0.0276	-0.0495	0.3492	-0.0548	0.0149	0.1097	0.2109	0.1434	-0.4413	-0.0851	0.1327	-0.2521	-0.1101	0.0073	0.51	0.1332	-0.0112	0.1872	-0.0181	0.2205	-3.1822	112.2133	7.7484
3	0.4551	-0.0002	-0.1124	0.7297	-0.4146	0.3152	-0.0187	0.1764	-0.0441	-0.4094	-0.0605	-0.4432	-0.0216	0.0936	-0.0209	0.3506	0.1062	0.1323	0.1348	0.0187	0.3305	9.1624	107.4337	13.8703
4	0.4739	0.0575	0.1819	0.7823	-0.1884	0.8407	-0.0804	0.327	0.3758	-0.6847	-0.1558	-0.5812	-0.3666	0.1605	-0.7925	0.5011	0.071	0.1805	-0.0087	0.0904	0.4727	10.9139	120.0965	11.0371
5	1.6046	-0.1271	-0.0813	1.1055	-0.5548	1.6901	0.0445	-0.1274	0.1715	-0.2273	-0.0735	-1.0229	-0.2152	0.273	-0.1224	0.3449	0.0442	0.1641	0.2111	0.0652	0.7623	20.9085	110.7272	14.3198
6	0.0983	-0.2249	0.0326	0.847	-0.3654	0.4298	-0.0156	0.07	0.0985	-0.5347	-0.0659	-0.6978	-0.049	0.2228	0.0574	0.4398	0.0665	0.1343	0.1791	0.0255	0.3807	10.5973	109.1475	10.9442
7	1.0066	0.2378	0.6369	0.2041	0.253	0.471	-0.1612	-0.2229	0.2501	0.01	-0.1481	-0.4695	0.2854	0.1246	-0.0895	0.3777	0.0862	0.1471	0.2024	0.056	0.442	12.5119	93.3727	20.1201
8	0.4525	-0.026	0.0955	0.4565	0.4515	0.4666	-0.0817	-0.051	0.1571	0.1682	0.0479	0.2259	-0.138	0.0049	-0.0754	0.311	0.0547	0.0825	0.132	0.023	0.213	5.7357	83.6162	16.6789
9	0.5025	-0.3754	-0.1774	1.2821	0.052	0.3289	-0.0959	-0.3103	0.0194	0.3122	0.211	-0.1105	-0.1448	0.3886	-0.0937	0.2752	0.0797	-0.049	0.2611	-0.0714	0.213	25.5385	71.7624	13.7213
10	0.1478	-0.1971	-0.1442	0.6253	0.058	0.1806	0.0654	0.1329	-0.1358	0.1034	0.0376	0.1602	0.0005	-0.159	-0.0929	0.2291	0.0633	0.0094	0.2232	0.0063	0.2363	10.2689	71.3688	8.6699
11	0.4374	-0.1139	-0.1668	1.0925	0.0309	0.8854	0.1138	0.1285	0.0391	-0.2999	0.0329	-0.1651	0.0612	0.1837	-0.106	0.2783	0.0472	0.0183	0.2639	-0.0296	0.1988	20.5475	69.9874	-0.727
12	0.6976	-0.3057	0.457	2.9426	0.1129	1.5438	0.0985	0.1836	-0.0048	-0.7316	-0.0755	0.4018	-0.1767	-0.5408	-0.0239	0.3368	0.0554	-0.0214	0.2841	0.0033	0.138	11.3698	76.7826	-6.1093
13	0.3949	-0.064	-0.3669	0.6133	0.1186	0.7906	0.0829	0.0998	0.0274	-0.124	0.1054	0.0251	-0.285	0.0465	-0.1321	0.2817	0.0158	0.0267	0.1887	-0.0448	0.1858	16.6416	76.4121	3.1507
14	0.8712	-0.3256	0.0534	0.8923	0.2016	0.069	0.3394	0.2148	0.0829	0.0389	-0.1126	0.1419	-0.2131	-0.0622	-0.0898	0.3849	0.0859	0.0762	0.2205	0.0743	0.2885	2.4647	85.8997	10.5112

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 275:294)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 295:313)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 314:335)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 336:390)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 391:461)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 462:493)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 494:511)
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 275:294)
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 295:313)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 314:324)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 325:390)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 391:461)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 462:493)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 494:512)

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