PDB-7ef0: Crystal structure of maize SHH2 SAWADEE domain in complex with an...

ID or keywords:

Entry

Database: PDB / ID: 7ef0

Title

Crystal structure of maize SHH2 SAWADEE domain in complex with an H3K9M 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: 1.5 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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PDBx/mmCIF format	7ef0.cif.gz	144.4 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ef/7ef0 ftp://data.pdbj.org/pub/pdb/validation_reports/ef/7ef0	HTTPS FTP

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Related structure data

Related structure data	7eezSC 7ef1C 7ef2C 7ef3C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2rq6-d 4kf6-3 2mu3-d 3znh-d 3omw-2 5xgr-2 4i7j-2 3fdf-4 5fv5-d 1wr6-1 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

hetero molecules

38.4 kDa, 3 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
20.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: HB transcription factor

hetero molecules

defined by author&software
Evidence: gel filtration
18.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	46.405, 50.032, 133.677
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: 18101.371 Da / Num. of mol.: 2 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: 2079.431 Da / Num. of mol.: 1 / Mutation: K9M / 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 / Water Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.18 Å³/Da / Density % sol: 39.31 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bicine, pH 8.5, 25% PEG 300

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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: May 24, 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: 1.5→50 Å / Num. obs: 51003 / % possible obs: 100 % / Redundancy: 8 % / R_merge(I) obs: 0.102 / R_pim(I) all: 0.039 / R_rim(I) all: 0.11 / Χ²: 2.335 / Net I/σ(I): 8.4 / Num. measured all: 405599

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
1.5-1.55	8	0.558	5040	0.885	0.209	0.596	1.571	100
1.55-1.62	8	0.445	4994	0.928	0.167	0.476	1.671	100
1.62-1.69	8.1	0.355	5020	0.952	0.133	0.379	1.734	100
1.69-1.78	8.1	0.262	5034	0.969	0.098	0.28	1.864	100
1.78-1.89	8.1	0.202	5047	0.981	0.076	0.216	2.086	100
1.89-2.04	8.1	0.153	5079	0.987	0.058	0.163	2.428	100
2.04-2.24	8	0.12	5086	0.991	0.045	0.129	2.59	100
2.24-2.56	8	0.101	5112	0.993	0.038	0.108	2.821	100
2.56-3.23	7.8	0.084	5176	0.995	0.032	0.09	3.239	100
3.23-50	7.4	0.064	5415	0.996	0.025	0.069	3.359	99.8

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7EEZ

7eez

Resolution: 1.5→38.119 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.94 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2082	2568	5.06 %
R_work	0.1793	48198	-
obs	0.1808	50766	99.98 %

Solvent computation

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

Displacement parameters

B_iso max: 58.26 Å² / B_iso mean: 17.6228 Å² / B_iso min: 5.92 Å²

Refinement step

Cycle: final / Resolution: 1.5→38.119 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2463	0	2	265	2730
B_iso mean	-	-	11.66	22.15	-
Num. residues	-	-	-	-	304

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	2511
X-RAY DIFFRACTION	f_angle_d	1.07	3383
X-RAY DIFFRACTION	f_chiral_restr	0.044	356
X-RAY DIFFRACTION	f_plane_restr	0.005	450
X-RAY DIFFRACTION	f_dihedral_angle_d	13.014	949

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / % reflection obs: 100 %

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work
1.5-1.5289	0.2404	140	0.21	2635
1.5289-1.5601	0.2501	151	0.1988	2650
1.5601-1.594	0.2258	143	0.1909	2618
1.594-1.6311	0.2121	132	0.1866	2635
1.6311-1.6719	0.2133	153	0.1838	2665
1.6719-1.7171	0.2116	158	0.1731	2618
1.7171-1.7676	0.2124	137	0.1685	2634
1.7676-1.8247	0.1839	117	0.1713	2660
1.8247-1.8899	0.1893	119	0.175	2693
1.8899-1.9655	0.2053	129	0.1721	2666
1.9655-2.055	0.2159	142	0.1766	2671
2.055-2.1633	0.1922	143	0.1753	2657
2.1633-2.2988	0.1964	153	0.1713	2677
2.2988-2.4763	0.2082	163	0.1859	2656
2.4763-2.7254	0.221	146	0.1982	2716
2.7254-3.1197	0.2311	144	0.1935	2719
3.1197-3.9298	0.2	137	0.1738	2746
3.9298-38.119	0.1985	161	0.1679	2882

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	2.462	-1.099	-2.1586	4.623	1.6274	4.9429	-0.0321	0.1481	0.5559	-0.0776	0.0498	0.3044	-0.5049	-0.3963	-0.0082	0.1153	0.0194	0.0014	0.1004	0.0305	0.1648	5.0119	27.0558	61.9578
2	2.8771	-0.0193	0.0934	2.8516	-0.6963	3.0407	-0.0965	-0.0012	0.0376	0.1422	0.1069	0.022	-0.2742	0.0143	-0.0107	0.0754	0.0109	-0.0081	0.0778	-0.0226	0.0677	9.0118	23.2915	68.2095
3	4.5181	0.882	-1.7412	1.5605	-0.7831	4.1296	0.0054	-0.1961	0.365	0.084	-0.0406	-0.0089	-0.5747	0.429	-0.0011	0.2085	-0.0617	-0.0244	0.1627	-0.0393	0.1482	14.2391	31.9297	68.9667
4	1.9112	1.9664	0.4589	3.8975	0.8824	4.8817	-0.1981	0.0849	0.0438	-0.196	0.166	-0.2412	-0.3858	0.4687	0.022	0.0934	-0.0384	0.0105	0.1216	-0.0291	0.103	14.7524	26.8552	62.7131
5	0.6046	1.2055	1.369	2.2312	2.5251	3.438	-0.0134	-0.0785	0.1786	-0.0988	-0.1748	0.2674	-0.0586	-0.2702	0.1641	0.0961	-0.005	-0.0014	0.1109	0.0154	0.1021	-0.2946	14.9703	51.4901
6	5.4133	-0.2498	-0.2073	4.1196	-1.0581	6.1306	-0.0305	-0.4617	-0.2952	0.5019	0.1156	-0.0747	0.5086	-0.1912	0.058	0.171	-0.0166	-0.0281	0.1026	0.004	0.1027	4.4921	9.9363	66.2815
7	2.9388	0.7011	0.4755	0.7463	1.4674	1.6633	0.0553	0.1379	-0.1578	0.0854	-0.0312	0.0121	0.2242	-0.0771	-0.025	0.101	-0.0191	-0.0106	0.0622	0.0333	0.0657	-1.6817	7.0905	54.6714
8	3.9558	-0.3546	3.8101	3.933	1.7542	7.0883	0.1337	-0.0516	-0.2996	0.1836	0.2099	-0.1891	0.2948	0.2778	-0.2531	0.0838	0.0194	-0.0145	0.0811	0.0034	0.0889	8.8812	5.8438	59.3677
9	4.3281	0.0064	0.2481	5.6104	0.5272	1.5961	0.059	-0.1182	-0.1652	0.0892	-0.0538	0.2192	0.146	-0.0483	-0.0457	0.074	-0.0271	-0.0143	0.115	0.006	0.0338	0.7875	8.7709	58.3365
10	5.0725	2.4598	1.7666	4.8847	2.1417	4.7366	-0.1783	0.2075	0.0924	-0.3205	0.0049	0.4728	-0.1244	-0.35	0.2082	0.1262	-0.0117	-0.0012	0.1622	0.008	0.1256	-0.7291	17.1014	43.7091
11	1.9451	-1.6691	-0.0594	3.9465	1.2928	2.885	0.0464	0.1415	-0.127	-0.1242	-0.1438	0.3798	-0.3389	-0.4051	-0.0009	0.1567	0.0135	-0.0039	0.1503	-0.0119	0.1511	5.1893	26.4327	37.0246
12	0.978	-0.0985	0.3494	2.3927	-1.142	3.3814	0.0476	0.067	-0.0486	-0.0854	0.1181	0.2085	0.0504	-0.1449	-0.1604	0.0673	-0.0004	0.0008	0.081	0.0059	0.093	5.9465	17.139	31.2238
13	1.2245	1.2529	1.4296	1.4872	2.5204	2.847	-0.0106	0.0356	0.095	-0.0797	0.0223	-0.0013	-0.1524	0.1563	0.018	0.1334	-0.0386	-0.0065	0.0912	0.0255	0.1055	15.056	27.6014	41.8577
14	2.5271	0.6871	-0.1749	1.9661	0.2764	1.4158	-0.0099	0.0934	0.1615	0.0295	0.0678	-0.1496	-0.0956	0.0527	-0.0507	0.1223	-0.0341	-0.0175	0.0829	0.0189	0.1199	22.1158	34.0871	45.9505
15	6.1628	-2.4038	4.0216	4.0812	-2.7045	3.9173	0.0377	-0.62	-0.3222	0.2191	0.3056	0.0688	0.2356	-0.5316	-0.4243	0.1488	0.0099	0.0123	0.2494	0.0037	0.1835	1.014	14.8955	70.8983

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 133 through 139 )	A	133 - 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 188 )	A	178 - 188
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 189 through 205 )	A	189 - 205
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 206 through 216 )	A	206 - 216
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 217 through 239 )	A	217 - 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 261 )	A	251 - 261
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 262 through 279 )	A	262 - 279
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 126 through 145 )	B	126 - 145
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 146 through 177 )	B	146 - 177
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 178 through 217 )	B	178 - 217
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 218 through 272 )	B	218 - 272
15	X-RAY DIFFRACTION	15	chain 'P' and (resid 1 through 14 )	P	1 - 14

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