PDB-7ef2: Crystal structure of maize SHH2 SAWADEE domain in complex with an...

ID or keywords:

Entry

Database: PDB / ID: 7ef2

Title

Crystal structure of maize SHH2 SAWADEE domain in complex with an H3K9me3 peptide

Components

HB transcription factor
Histone H3.2

Keywords

GENE REGULATION / SAWADEE domain / Maize / SHH2

Function / homology

Function and homology information

chromocenter / structural constituent of chromatin / nucleosome / protein heterodimerization activity / chromatin binding / DNA binding / metal ion binding / nucleus
Similarity search - Function

Biological species

Zea mays (maize)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Wang, Y. / Du, J.

Funding support

China, 1items

Citation

Journal: J Integr Plant Biol / Year: 2021
Title: Recognition of H3K9me1 by maize RNA-directed DNA methylation factor SHH2.
Authors: Wang, Y. / Zhou, X. / Luo, J. / Lv, S. / Liu, R. / Du, X. / Jia, B. / Yuan, F. / Zhang, H. / Du, J.

History

Deposition	Mar 20, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 30, 2021	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 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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Download

PDBx/mmCIF format	7ef2.cif.gz	146.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7ef2.ent.gz	113.5 KB	Display	PDB format
PDBx/mmJSON format	7ef2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7ef2_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	7ef2_full_validation.pdf.gz	1.4 MB	Display
Data in XML	7ef2_validation.xml.gz	15.5 KB	Display
Data in CIF	7ef2_validation.cif.gz	21.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ef/7ef2 ftp://data.pdbj.org/pub/pdb/validation_reports/ef/7ef2	HTTPS FTP

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Related structure data

Related structure data	7eezSC 7ef0C 7ef1C 7ef3C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7ef1-1 2hqv-d 7ef3-2 3rf2-d 7ef3-1 6mx2-8 6mx2-13 6mx2-2 6rvc-3 6mx2-4 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
Related items in Molecule of the Month	#112 - Apr 2009 Oct and Sox Transcription Factors similarity (3) #7 - Jul 2000 Nucleosome similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

Deposited unit

A: HB transcription factor

B: HB transcription factor

P: Histone H3.2

Q: Histone H3.2

hetero molecules

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

1

A: HB transcription factor

P: Histone H3.2

hetero molecules

defined by author&software
Evidence: isothermal titration calorimetry
19.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: HB transcription factor

Q: Histone H3.2

hetero molecules

defined by author&software
Evidence: isothermal titration calorimetry
19.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	65.092, 68.254, 80.811
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	HB transcription factor / Protein SAWADEE HOMEODOMAIN HOMOLOG 2 Mass: 18001.229 Da / Num. of mol.: 2 / Mutation: R235G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zea mays (maize) / Gene: 100279552, HB131, ZEAMMB73_Zm00001d005584 / Plasmid: pET-Sumo / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7ZYP9
#2: Protein/peptide	Histone H3.2 Mass: 1192.412 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Zea mays (maize) / References: UniProt: P69246
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.54 Å³/Da / Density % sol: 51.58 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES, pH7.5, 70% MPD

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL19U1 / Wavelength: 0.9792 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 7, 2015

Radiation

Monochromator: silicon crystal (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9792 Å / Relative weight: 1

Reflection

Resolution: 2→50 Å / Num. obs: 25032 / % possible obs: 99 % / Redundancy: 7 % / R_merge(I) obs: 0.085 / R_pim(I) all: 0.035 / R_rim(I) all: 0.092 / Χ²: 2.029 / Net I/σ(I): 11.7 / Num. measured all: 175521

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2-2.07	6.4	0.519	2319	0.887	0.219	0.565	1.479	93.5
2.07-2.15	7.3	0.424	2475	0.945	0.167	0.456	1.557	99.4
2.15-2.25	7.3	0.292	2475	0.969	0.115	0.314	1.586	99.6
2.25-2.37	7.3	0.23	2488	0.98	0.091	0.247	1.685	99.8
2.37-2.52	7.3	0.183	2483	0.986	0.072	0.197	1.702	99.8
2.52-2.71	7.2	0.133	2521	0.992	0.053	0.143	1.872	99.8
2.71-2.99	7.2	0.094	2510	0.996	0.038	0.101	2.083	100
2.99-3.42	7.1	0.065	2537	0.998	0.026	0.071	2.372	100
3.42-4.31	6.7	0.056	2576	0.998	0.024	0.061	3.095	100
4.31-50	6.4	0.047	2648	0.998	0.02	0.051	2.892	98

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-2000		data scaling
PDB_EXTRACT	3.27	data extraction
HKL-2000		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7EEZ

7eez

Resolution: 2→30.669 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.58 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2446	1260	5.09 %
R_work	0.2147	23500	-
obs	0.2162	24760	99.21 %

Solvent computation

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

Displacement parameters

B_iso max: 106.21 Å² / B_iso mean: 38.7053 Å² / B_iso min: 15.32 Å²

Refinement step

Cycle: final / Resolution: 2→30.669 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2476	0	2	204	2682
B_iso mean	-	-	38.63	45.26	-
Num. residues	-	-	-	-	305

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	2523
X-RAY DIFFRACTION	f_angle_d	0.733	3401
X-RAY DIFFRACTION	f_chiral_restr	0.027	357
X-RAY DIFFRACTION	f_plane_restr	0.003	450
X-RAY DIFFRACTION	f_dihedral_angle_d	14.093	951

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
2.0001-2.0801	0.2848	117	0.2468	2484	96
2.0801-2.1748	0.2744	143	0.2451	2574	100
2.1748-2.2894	0.2493	138	0.22	2583	100
2.2894-2.4328	0.2634	154	0.2253	2593	100
2.4328-2.6205	0.2599	131	0.2393	2615	100
2.6205-2.8841	0.2707	143	0.2299	2610	100
2.8841-3.301	0.2419	146	0.2139	2625	100
3.301-4.1572	0.2072	141	0.1871	2668	100
4.1572-30.669	0.2413	147	0.2097	2748	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	8.4462	6.247	-3.0409	8.433	-3.1467	6.8995	-0.0835	0.3111	-0.0635	0.1166	0.3353	0.4467	0.4625	-1.0206	-0.2574	0.2795	-0.0642	-0.0102	0.3275	0.0064	0.2461	-21.3966	10.5162	-14.5619
2	7.9362	0.6757	2.1651	4.2729	1.6896	3.057	-0.0865	0.0385	0.5769	-0.4312	-0.2125	0.0016	-0.4062	0.0491	0.2549	0.2164	0.0105	-0.008	0.1605	0.0575	0.1701	-15.3772	20.1217	-18.0459
3	5.6139	0.4117	0.5727	4.6674	1.6984	6.9337	-0.0105	0.2889	0.2973	-0.2271	0.2282	-0.3036	-0.6367	0.0756	-0.1432	0.3673	-0.0249	-0.0295	0.2294	-0.0032	0.2004	-16.5107	17.2043	-27.4118
4	3.2592	-0.1345	0.4908	4.3667	-2.5529	2.4793	0.1056	-0.0988	-0.0446	-0.3185	0.0423	0.2269	-0.0795	-0.0962	-0.1253	0.181	-0.0139	-0.0392	0.2011	-0.0058	0.1982	-15.202	13.197	-15.7941
5	4.7952	-1.6693	0.685	3.9958	-2.0865	6.0083	-0.244	-0.1821	0.261	0.3809	0.1583	-0.0298	-0.4583	0.0708	0.0379	0.1737	0.0052	-0.0115	0.1927	-0.0757	0.1968	-10.4257	18.6436	-1.7286
6	3.888	1.298	1.2349	2.0286	-1.2714	2.1856	-0.366	-1.5385	1.1878	1.1141	0.4268	0.1739	-0.2741	-0.1761	-0.3002	0.7763	0.1226	0.221	0.4917	-0.0491	0.4	-17.177	18.0109	13.4991
7	8.0883	2.2759	-1.9597	7.1511	-3.4074	6.4815	-0.0263	-0.2482	0.4126	0.2451	0.0325	-0.4448	-0.4007	0.5175	-0.1411	0.1526	-0.0358	-0.0279	0.1856	-0.074	0.251	-3.786	20.4152	-1.9991
8	2.141	-0.6604	0.5093	4.5711	2.9899	5.5297	-0.1627	-0.2314	0.2	0.1131	0.1442	-0.1232	-0.3756	0.0741	0.0913	0.1811	0.0333	0.02	0.2269	-0.0138	0.1839	-12.3147	19.2031	0.1613
9	4.8294	3.7576	-3.7824	8.0348	-4.6035	3.6562	0.2551	-0.021	-0.3772	0.7095	0.4387	0.5893	-0.3764	-0.8824	-0.6971	0.2414	-0.0193	0.049	0.3526	0.0638	0.3466	-19.6972	0.8556	3.1165
10	7.7819	5.2097	3.0771	7.1651	1.1032	8.6814	0.021	0.0093	-0.6533	-0.2749	-0.1989	-0.1196	0.6482	-0.5291	0.0636	0.2552	0.0039	0.0568	0.3834	0.0228	0.2742	-8.9673	-8.1675	5.1986
11	4.1168	2.1439	-2.1107	1.6727	-2.5982	5.3722	0.3541	-0.7502	0.3139	0.4349	-0.4678	-0.1354	-0.5174	0.9679	0.0198	0.2758	-0.0353	0.0193	0.4264	0.0092	0.3242	-0.6723	-4.1984	15.2378
12	4.2079	0.6948	0.2479	5.2362	-0.9502	5.923	0.3982	-0.5189	-0.279	-0.0911	-0.1499	-1.2482	0.8296	1.7342	-0.0298	0.398	0.1442	0.0606	0.6912	0.1351	0.4106	2.8951	-12.292	14.0557
13	3.3411	0.1528	2.3854	3.1038	-2.3203	7.3892	-0.0419	-0.303	0.0582	-0.0615	-0.0925	-0.0294	-0.1688	0.008	-0.0455	0.1555	0.0056	0.0645	0.2534	0.0347	0.2617	-3.6179	-3.9451	6.6526
14	4.5129	-0.255	-0.1806	4.6197	-0.1297	4.7158	-0.1212	0.1207	-0.5471	-0.3226	-0.14	-0.4881	0.251	0.7448	-0.0472	0.1808	0.0081	0.131	0.3299	0.0018	0.3054	2.2503	-2.3421	-7.8441
15	2.6566	-0.157	0.7201	3.4959	1.8929	5.3688	0.0144	0.4329	-0.254	-0.7033	-0.1568	-0.0732	-0.3567	0.2287	0.0187	0.2582	-0.0086	0.087	0.3008	-0.0661	0.2992	1.9311	-1.9853	-14.6679
16	3.8102	0.7874	3.7735	3.171	1.0516	4.9357	0.0039	0.1977	-0.2162	-0.0367	0.3597	-0.2136	0.0471	0.4699	0.0242	0.1918	-0.0511	0.0896	0.2622	-0.0764	0.2511	6.9696	4.7003	-6.7393
17	4.3756	0.54	-1.8304	2.6478	1.0814	5.7077	-0.2866	0.4877	-0.7163	-0.267	0.3318	-0.5801	0.251	0.0886	0.122	0.2365	-0.0053	0.0919	0.2658	-0.1183	0.2767	3.764	-2.77	-10.2812
18	2.1603	-2.0484	3.9395	8.0131	-1.5946	9.2036	0.2011	0.4351	-0.4632	-0.5939	-0.0048	1.1436	0.4565	-0.5872	-0.2326	0.2912	-0.083	0.001	0.3874	-0.0378	0.4126	-13.7553	-1.1432	-8.0686
19	7.4718	-1.5228	-0.1521	9.4817	-3.4134	6.1816	0.4313	-0.8208	-0.3607	0.9861	0.1288	1.3663	-0.6536	-0.1932	-0.6083	0.3539	-0.003	0.0713	0.3724	-0.0015	0.4213	-20.7953	23.2286	-6.8139
20	9.6196	1.4921	0.9663	7.5303	-2.3565	1.8107	0.0953	0.6559	-1.8072	-1.2482	-0.1302	-0.9349	0.8944	1.649	0.3716	0.5276	0.0297	0.0868	0.5339	-0.0707	0.801	5.5914	-12.6049	-2.6053

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 131 through 139 )	A	131 - 139
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 140 through 152 )	A	140 - 152
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 153 through 177 )	A	153 - 177
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 178 through 194 )	A	178 - 194
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 195 through 228 )	A	195 - 228
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 229 through 239 )	A	229 - 239
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 240 through 250 )	A	240 - 250
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 251 through 262 )	A	251 - 262
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 263 through 278 )	A	263 - 278
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 131 through 139 )	B	131 - 139
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 140 through 163 )	B	140 - 163
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 164 through 177 )	B	164 - 177
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 178 through 194 )	B	178 - 194
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 195 through 216 )	B	195 - 216
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 217 through 239 )	B	217 - 239
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 240 through 250 )	B	240 - 250
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 251 through 261 )	B	251 - 261
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 262 through 272 )	B	262 - 272
19	X-RAY DIFFRACTION	19	chain 'P' and (resid 2 through 8 )	P	2 - 8
20	X-RAY DIFFRACTION	20	chain 'Q' and (resid 3 through 8 )	Q	3 - 8

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