PDB-7ef1: crystal structure of maize SHH2 SAWADEE domain in complex with an...

ID or keywords:

Entry

Database: PDB / ID: 7ef1

Title

crystal structure of maize SHH2 SAWADEE domain in complex with and H3K9me1 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 /

nucleus
Similarity search - Function

Biological species

Zea mays (maize)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 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	7ef1.cif.gz	146.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7ef1.ent.gz	113.6 KB	Display	PDB format
PDBx/mmJSON format	7ef1.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/ef/7ef1 ftp://data.pdbj.org/pub/pdb/validation_reports/ef/7ef1	HTTPS FTP

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Related structure data

Related structure data	7eezSC 7ef0C 7ef2C 7ef3C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7ef3-1 7ef2-1 6mx2-7 6mx2-8 7ef3-2 6mx2-6 2agm-d 3byi-1 6mx2-2 1h6h-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
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

38.3 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
19.1 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
19.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	64.821, 68.563, 80.976
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: 17914.150 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: 1163.351 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
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 234 / 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: 51.65 %
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: Jun 28, 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: 1.9→50 Å / Num. obs: 29252 / % possible obs: 99.6 % / Redundancy: 4 % / R_merge(I) obs: 0.102 / R_pim(I) all: 0.055 / R_rim(I) all: 0.116 / Χ²: 1.043 / Net I/σ(I): 7.4 / Num. measured all: 116568

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
1.9-1.97	3.9	0.757	2883	0.741	0.421	0.869	0.771	99.5
1.97-2.05	4	0.593	2862	0.831	0.32	0.676	0.846	99.3
2.05-2.14	4.1	0.469	2873	0.879	0.248	0.532	0.862	99.4
2.14-2.25	4	0.341	2892	0.934	0.181	0.388	0.932	99.8
2.25-2.39	4.1	0.263	2877	0.962	0.14	0.299	0.951	99.6
2.39-2.58	4	0.205	2909	0.971	0.11	0.233	1.006	99.8
2.58-2.84	4	0.149	2942	0.98	0.081	0.17	1.215	99.9
2.84-3.25	4	0.09	2958	0.993	0.05	0.103	1.33	100
3.25-4.09	3.9	0.046	2951	0.998	0.026	0.053	1.274	99
4.09-50	3.9	0.034	3105	0.998	0.019	0.04	1.227	99.2

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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: 1.9→34.863 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 20.86 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2259	1476	5.09 %
R_work	0.1912	27505	-
obs	0.193	28981	99.6 %

Solvent computation

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

Displacement parameters

B_iso max: 91.44 Å² / B_iso mean: 32.5679 Å² / B_iso min: 12.66 Å²

Refinement step

Cycle: final / Resolution: 1.9→34.863 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2478	0	2	234	2714
B_iso mean	-	-	26.36	38.91	-
Num. residues	-	-	-	-	306

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	2525
X-RAY DIFFRACTION	f_angle_d	0.877	3399
X-RAY DIFFRACTION	f_chiral_restr	0.034	358
X-RAY DIFFRACTION	f_plane_restr	0.003	451
X-RAY DIFFRACTION	f_dihedral_angle_d	13.941	953

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 (%)
1.9-1.9613	0.2331	113	0.2157	2483	99
1.9613-2.0314	0.2265	149	0.207	2426	99
2.0314-2.1127	0.2264	147	0.2043	2425	100
2.1127-2.2089	0.2336	143	0.2008	2486	100
2.2089-2.3253	0.2201	124	0.1838	2479	100
2.3253-2.471	0.2246	126	0.1906	2496	100
2.471-2.6617	0.2274	146	0.1957	2468	100
2.6617-2.9294	0.2213	130	0.1935	2518	100
2.9294-3.353	0.2512	143	0.1903	2516	100
3.353-4.2233	0.1959	123	0.1673	2533	99
4.2233-34.863	0.2336	132	0.2001	2675	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	3.5711	4.406	-1.3609	5.5862	-2.1672	6.4274	0.451	0.0823	0.0782	0.4441	-0.0919	0.3978	0.1716	-0.4351	-0.3353	0.2649	-0.0097	-0.0278	0.2212	-0.0073	0.2558	-21.4168	10.4273	-14.566
2	6.1553	2.4465	2.0218	2.2907	2.2993	5.1594	0.2193	0.0066	0.4003	-0.1426	-0.3234	0.0893	-0.2531	-0.1466	0.0242	0.2089	0.0356	-0.0171	0.1155	0.033	0.2003	-15.2418	20.2432	-17.8686
3	3.8847	1.0881	0.6958	5.1419	1.4964	6.5945	-0.0343	0.5806	-0.2365	-0.2983	0.5048	-0.8717	0.0319	0.7711	-0.2645	0.2744	-0.0434	0.0071	0.3076	-0.1171	0.2526	-12.2592	10.5333	-31.958
4	3.4795	-0.0385	0.1676	6.9384	1.2236	5.0634	0.3146	0.2489	0.6267	-0.8245	-0.3353	0.0102	-1.0542	-0.6242	-0.0014	0.3761	0.0691	-0.0427	0.2524	0.0016	0.2142	-19.6993	22.4316	-23.5541
5	3.783	-0.2096	0.0233	1.9645	-1.2222	2.0941	-0.0416	0.0323	-0.0994	-0.1793	0.0408	0.0449	0.2051	-0.196	0.0255	0.1585	-0.0098	-0.0246	0.1344	-0.0034	0.163	-15.1991	13.1714	-15.7726
6	3.8157	-1.2142	0.3677	2.8371	-0.9749	4.0049	-0.1727	-0.1791	0.1994	0.1585	0.0407	-0.0202	-0.329	-0.0111	0.0959	0.1487	0.0083	-0.0225	0.1476	-0.0496	0.1484	-10.5061	18.616	-1.7203
7	6.3064	2.2351	-0.5926	1.1564	-1.7199	6.7861	-0.5211	-1.3395	1.0385	1.3583	0.686	0.5949	-0.2366	-0.3969	-0.0195	0.5027	0.0946	0.0964	0.4361	-0.0366	0.3508	-17.1546	18.0169	13.4689
8	4.7591	1.452	-2.572	4.9108	-1.8292	7.1545	0.0103	-0.4324	0.5437	0.1258	-0.0514	-0.1964	-0.2842	0.3955	0.0947	0.1294	0.003	-0.045	0.1522	-0.0382	0.2048	-3.7935	20.3943	-2.036
9	1.4528	0.8489	0.5504	3.3273	2.0823	3.8104	-0.0405	-0.0229	0.1546	0.1576	0.1041	-0.172	-0.1874	0.0835	-0.0594	0.1721	0.0522	-0.0014	0.1705	-0.0213	0.1906	-12.3281	19.1864	0.1364
10	5.5087	5.0124	-5.2122	6.8372	-5.0418	8.515	0.1593	-0.053	-0.2698	0.7082	0.3196	0.7394	-0.1461	-0.7382	-0.3776	0.2343	-0.0082	0.0512	0.2806	0.0772	0.3288	-19.6903	0.8871	3.1207
11	9.2118	8.2913	2.1286	9.1498	1.6879	4.5593	0.1322	0.0969	-0.5166	-0.2033	-0.1315	0.0291	0.3126	-0.1924	0.1503	0.2142	-0.0053	0.0239	0.301	0.0497	0.2272	-8.9862	-8.2152	5.1225
12	4.6185	3.077	-2.299	3.4197	-2.3288	5.6077	-0.0388	-0.4946	-0.1799	0.0741	-0.2916	-0.2515	0.0616	0.8718	0.1338	0.1793	0.0524	0.0234	0.3255	0.0722	0.2135	2.4501	-6.9384	8.4988
13	5.325	0.9593	-1.7767	3.7231	-1.0275	7.5343	0.3512	-0.3507	0.5132	0.2614	-0.3061	-0.5533	-0.067	1.0721	-0.1561	0.1906	-0.0327	0.0199	0.4036	0.0796	0.2718	-0.2478	-7.3882	17.6962
14	3.0374	0.4492	2.0812	1.9109	-1.6906	7.6128	0.0752	-0.2753	-0.1144	0.0257	-0.0002	-0.0307	-0.1576	-0.0856	-0.0792	0.1379	-0.0045	0.036	0.2114	0.0253	0.226	-3.7899	-3.9335	6.6104
15	4.2665	0.2415	-0.3121	3.5845	0.5632	3.1268	-0.0187	-0.0841	-0.3296	-0.2451	-0.043	-0.2243	0.0355	0.5581	0.0213	0.1497	0.0046	0.0673	0.2158	-0.0025	0.1887	2.8128	-0.8441	-7.3777
16	4.4807	-0.9686	1.408	3.3484	4.898	9.0768	0.3675	0.6803	-0.3756	-0.8694	-0.5874	-0.0628	-0.3751	-0.1615	0.1116	0.3701	0.0326	0.0297	0.2892	-0.086	0.2735	-0.0424	-5.8242	-23.013
17	3.9157	0.322	0.693	2.4686	0.5673	4.0707	-0.1874	0.1781	-0.087	-0.3576	0.2955	-0.3012	-0.1061	0.3962	-0.1216	0.1682	-0.0204	0.0685	0.1545	-0.0542	0.1972	5.3019	1.0335	-8.5336
18	2.5369	-0.9481	2.1403	8.1939	-1.4529	3.9955	0.1681	0.3807	-0.5226	-0.5976	0.0102	1.1936	0.4063	-1.0461	-0.2769	0.2321	-0.0554	-0.0305	0.3466	-0.0503	0.3569	-13.8402	-1.1031	-8.1172
19	7.1764	1.4091	-2.5995	7.7121	-4.6388	3.4309	0.5007	-0.8257	0.1124	0.7175	0.0133	1.2033	-0.3831	0.294	-0.4029	0.3635	-0.0371	0.0169	0.2509	-0.0049	0.3554	-19.1297	25.064	-8.8026
20	2.3234	0.3728	0.2836	7.4989	0.1725	2.8526	-0.2327	0.451	-1.5905	-1.1341	0.239	-0.8745	0.396	1.41	-0.099	0.4206	0.0887	0.116	0.4413	-0.018	0.5329	5.4642	-12.4818	-2.5644

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 163 )	A	153 - 163
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 164 through 177 )	A	164 - 177
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 178 through 194 )	A	178 - 194
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 195 through 228 )	A	195 - 228
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 229 through 239 )	A	229 - 239
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 240 through 250 )	A	240 - 250
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 251 through 262 )	A	251 - 262
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 263 through 278 )	A	263 - 278
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 131 through 139 )	B	131 - 139
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 140 through 152 )	B	140 - 152
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 153 through 177 )	B	153 - 177
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 178 through 194 )	B	178 - 194
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 195 through 228 )	B	195 - 228
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 229 through 239 )	B	229 - 239
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 240 through 261 )	B	240 - 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 10 )	P	2 - 10
20	X-RAY DIFFRACTION	20	chain 'Q' and (resid 3 through 8 )	Q	3 - 8

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