PDB-8j0h: Crystal structure of the fission yeast Rex1BD protein(C4H3.06)

ID or keywords:

Entry

Database: PDB / ID: 8j0h

Title

Crystal structure of the fission yeast Rex1BD protein(C4H3.06)

Components

Uncharacterized protein C4H3.06

Keywords

NUCLEAR PROTEIN / Heterochromatin / DNA repair / Histone deacetylase / protein-protein interaction

Function / homology

Required for excision 1-B domain-containing protein / DNA repair REX1-B / nucleus / cytosol / Uncharacterized protein C4H3.06

Function and homology information

Biological species

Schizosaccharomyces pombe (fission yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3.383 Å

Authors

Li, J. / Sun, W. / Chen, Y.

Funding support

China, 1items

Citation

Journal: Nat Commun / Year: 2024
Title: The SUN-family protein Sad1 mediates heterochromatin spatial organization through interaction with histone H2A-H2B.
Authors: Sun, W. / Dong, Q. / Li, X. / Gao, J. / Ye, X. / Hu, C. / Li, F. / Chen, Y.

History

Deposition	Apr 11, 2023	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Nov 1, 2023	Provider: repository / Type: Initial release
Revision 1.1	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.2	May 29, 2024	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8j0h.cif.gz	426.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8j0h.ent.gz	360.8 KB	Display	PDB format
PDBx/mmJSON format	8j0h.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8j0h_validation.pdf.gz	419.5 KB	Display	wwPDB validaton report
Full document	8j0h_full_validation.pdf.gz	435.1 KB	Display
Data in XML	8j0h_validation.xml.gz	19.5 KB	Display
Data in CIF	8j0h_validation.cif.gz	30.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j0/8j0h ftp://data.pdbj.org/pub/pdb/validation_reports/j0/8j0h	HTTPS FTP

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Related structure data

Related structure data	7ybfC C: citing same article (ref.)
Similar structure data	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

Deposited unit

A: Uncharacterized protein C4H3.06

B: Uncharacterized protein C4H3.06

C: Uncharacterized protein C4H3.06

D: Uncharacterized protein C4H3.06

E: Uncharacterized protein C4H3.06

F: Uncharacterized protein C4H3.06

G: Uncharacterized protein C4H3.06

H: Uncharacterized protein C4H3.06

130 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Uncharacterized protein C4H3.06

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

2

B: Uncharacterized protein C4H3.06

defined by author
16.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Uncharacterized protein C4H3.06

defined by author
16.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Uncharacterized protein C4H3.06

defined by author
16.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

E: Uncharacterized protein C4H3.06

defined by author
16.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

F: Uncharacterized protein C4H3.06

defined by author
16.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

7

G: Uncharacterized protein C4H3.06

defined by author
16.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

8

H: Uncharacterized protein C4H3.06

defined by author
16.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	159.014, 138.481, 50.897
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Uncharacterized protein C4H3.06 / Rex1BD Mass: 16258.812 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Details: GP is the 3C protease cleavage site, LGS are linkers. Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Gene: SPAC4H3.06 / Production host: Escherichia coli (E. coli) / References: UniProt: Q10214
Has ligand of interest	N

#1: Protein

Uncharacterized protein C4H3.06 / Rex1BD

Mass: 16258.812 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: GP is the 3C protease cleavage site, LGS are linkers.
Source: (gene. exp.)

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Gene: SPAC4H3.06 / Production host:

Escherichia coli (E. coli) / References: UniProt: Q10214

Has ligand of interest

N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.24 Å³/Da / Density % sol: 44.97 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 8%v/v Tacsimate pH5.0, 20%w/v polyethylene glycol 3350

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL19U1 / Wavelength: 0.9785 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 23, 2019

Radiation

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

Radiation wavelength

Wavelength: 0.9785 Å / Relative weight: 1

Reflection

Resolution: 3.38→50 Å / Num. obs: 30157 / % possible obs: 99.8 % / Redundancy: 3.5 % / CC_1/2: 0.998 / R_merge(I) obs: 0.129 / R_rim(I) all: 0.139 / Net I/σ(I): 13.43

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
3.39-3.59	0.652	4792	0.876	0.703	1
3.59-3.84	0.383	4587	0.946	0.414	1
3.84-4.14	0.224	4235	0.98	0.244	1
4.14-4.53	0.134	3962	0.994	0.144	1
4.53-5.06	0.101	3568	0.996	0.109	1
5.06-5.84	0.156	3099	0.989	0.168	1
5.84-7.12	0.116	2672	0.995	0.125	1
7.12-9.97	0.038	2074	0.999	0.041	1
9.97-50	0.027	1168	1	0.029	1

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Processing

Software

Name	Version	Classification
PHENIX	(1.14_3260: ???)	refinement
XDS		data scaling
XDS		data reduction
PHASES		phasing

Refinement

Method to determine structure:

SAD / Resolution: 3.383→48.474 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.96 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2961	2970	9.89 %
R_work	0.2416	-	-
obs	0.2471	30025	99.18 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.383→48.474 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8308	0	0	0	8308

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	8324
X-RAY DIFFRACTION	f_angle_d	0.469	11178
X-RAY DIFFRACTION	f_dihedral_angle_d	5.87	5390
X-RAY DIFFRACTION	f_chiral_restr	0.032	1370
X-RAY DIFFRACTION	f_plane_restr	0.002	1452

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 (%)
3.3832-3.4387	0.379	124	0.3448	1162	X-RAY DIFFRACTION	90
3.4387-3.498	0.4164	142	0.3338	1275	X-RAY DIFFRACTION	100
3.498-3.5616	0.425	137	0.3082	1307	X-RAY DIFFRACTION	100
3.5616-3.63	0.3693	151	0.3082	1305	X-RAY DIFFRACTION	100
3.63-3.7041	0.3551	139	0.3022	1281	X-RAY DIFFRACTION	100
3.7041-3.7846	0.3661	140	0.2917	1274	X-RAY DIFFRACTION	100
3.7846-3.8726	0.3201	147	0.2785	1322	X-RAY DIFFRACTION	100
3.8726-3.9694	0.2823	147	0.2595	1299	X-RAY DIFFRACTION	100
3.9694-4.0767	0.3529	144	0.2524	1282	X-RAY DIFFRACTION	99
4.0767-4.1966	0.2906	141	0.2403	1318	X-RAY DIFFRACTION	100
4.1966-4.332	0.2677	138	0.2313	1271	X-RAY DIFFRACTION	100
4.332-4.4867	0.2545	146	0.2148	1301	X-RAY DIFFRACTION	100
4.4867-4.6662	0.2857	143	0.2068	1301	X-RAY DIFFRACTION	100
4.6662-4.8784	0.2542	140	0.1978	1266	X-RAY DIFFRACTION	100
4.8784-5.1353	0.2963	146	0.2311	1337	X-RAY DIFFRACTION	100
5.1353-5.4566	0.3323	140	0.2795	1277	X-RAY DIFFRACTION	99
5.4566-5.8773	0.4265	143	0.3122	1314	X-RAY DIFFRACTION	100
5.8773-6.4675	0.3644	138	0.2958	1293	X-RAY DIFFRACTION	100
6.4675-7.4005	0.3292	142	0.2686	1294	X-RAY DIFFRACTION	100
7.4005-9.313	0.1946	142	0.1783	1291	X-RAY DIFFRACTION	99
9.313-48.474	0.2123	140	0.1663	1285	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	3.0536	-0.5838	0.5172	2.766	-0.2776	1.0834	0.0542	0.4883	-0.2448	-0.2424	0.3816	-0.6379	0.7486	0.1275	-0.1354	0.785	0.0019	-0.0059	0.6277	-0.1887	0.6413	7.6055	95.5871	52.3675
2	8.1459	-1.9539	2.1298	5.8811	-1.8844	2.8214	0.2068	0.5507	-0.5405	0.3823	-0.2265	0.3408	-0.4359	0.3463	-0.2639	0.3395	-0.0616	0.089	0.4414	-0.1073	0.5778	2.7136	101.7354	58.886
3	2.8828	-2.2689	-0.6795	6.701	3.5613	1.9326	-0.4874	-0.113	0.3326	0.1414	0.6445	-1.0604	-0.2001	0.2718	-0.0711	0.2859	-0.0517	0.0693	0.4062	-0.0015	0.7279	12.8339	108.1533	57.1093
4	3.5426	0.0422	-1.0083	2.6974	-1.2181	2.9273	-0.2703	0.2556	0.8976	-1.0101	0.8542	-1.0843	-0.5042	0.5671	-0.4731	0.5113	-0.1025	-0.0356	0.6386	0.041	0.7927	17.878	107.5198	50.7522
5	5.3069	0.1295	1.2862	7.3046	-2.397	7.3857	0.4732	0.2349	-0.0715	-0.1541	-0.1199	-0.5777	0.3848	0.6555	-0.4833	0.5738	-0.1362	-0.09	0.6932	-0.1207	0.0807	-0.7301	98.7615	85.017
6	4.1421	-5.449	-0.6496	7.9289	1.5178	5.3146	-0.142	-0.1352	1.8945	2.7829	-0.3133	-0.0533	-1.0439	-1.7337	-0.915	1.2406	0.1984	0.2844	1.02	0.1403	1.8143	-13.8779	117.0526	74.3015
7	6.3331	-3.2608	0.1611	6.9776	-2.5954	3.5093	-0.0732	-0.3753	0.5675	-0.0649	0.3794	-0.6733	0.7462	0.2347	-0.4195	0.7302	0.0388	-0.0067	0.4967	-0.0194	0.4728	-3.4552	94.7864	76.5837
8	2	-2.3695	1.1046	2	-3.6828	8.592	0.6743	-1.4701	0.3153	1.3744	-0.3433	3.4911	-0.5037	-0.1438	0.0588	1.9253	-0.1787	-0.4337	0.5297	-0.0051	1.5293	-29.2839	106.4609	69.5075
9	9.4414	-1.8365	1.4448	3.668	0.0703	5.8218	-0.185	-0.3853	0.4393	-0.0143	0.2829	0.3578	0.6778	-0.7553	-0.2873	0.7267	-0.1752	0.0279	0.4918	-0.0003	0.506	-14.681	92.1511	83.2444
10	4.0668	-2.0779	-0.4292	5.2565	1.1779	5.2625	0.2073	-0.1556	-1.2129	0.3693	0.3634	3.2621	-0.2787	-0.6197	-0.4556	0.3351	-0.143	-0.0621	0.4437	-0.003	0.7505	-12.7323	94.5969	64.3618
11	1.9207	-0.9502	1.0573	3.9386	0.8882	2.8016	0.0968	0.1491	-0.104	0.1262	0.27	-0.2765	-0.104	-0.1057	-0.3482	0.366	0.0029	0.0507	0.4014	0.0089	0.5319	-6.8076	91.1787	56.3006
12	4.3521	-0.7812	4.0068	4.8035	-0.1364	4.0402	0.3453	-0.0021	0.9753	0.2145	0.0553	-1.5267	0.3786	0.3193	-0.1512	0.685	-0.1158	-0.122	0.8637	-0.0428	0.7859	17.1071	108.4533	72.436
13	2.2681	-0.6378	1.5243	0.3454	-1.3395	5.2479	0.3618	-0.1359	0.0897	0.1444	-0.3023	-0.4981	0.164	0.2864	-0.0269	0.5023	-0.0684	-0.134	0.6742	-0.1438	0.9176	6.0783	108.966	75.2729
14	3.1956	1.9821	3.0444	4.1294	0.0863	4.6317	0.4804	-0.9393	1.442	0.6063	0.144	-1.1919	-0.6578	-0.0767	-0.2287	0.9093	-0.1671	-0.05	0.8238	-0.1993	0.8028	11.9816	113.5127	86.7175
15	3.0879	-2.2185	1.2638	2.2399	0.7965	4.1323	0.5651	-0.2225	0.6523	0.0166	-0.4081	0.1825	-0.5781	-0.1906	-0.2066	0.6492	-0.0668	-0.069	0.4921	-0.0328	0.9429	33.5969	77.5535	38.5095
16	3.3757	-0.8262	-2.6604	1.1172	0.0333	2.3558	1.1236	0.5341	-1.1597	0.4376	-0.6192	0.0826	-0.2377	-0.3501	-0.3938	0.6671	-0.0917	-0.1055	0.9124	-0.0723	0.6196	36.2857	73.0259	27.7166
17	5.9076	1.7874	-6.6477	0.6932	-2.1579	7.5731	1.2054	1.8705	0.3425	0.0616	0.0953	-0.2437	-0.6208	-0.8989	-1.0249	0.9257	0.0134	-0.075	0.8789	0.045	0.886	32.5222	79.1625	23.0792
18	4.5182	0.5482	0.6512	5.7714	-0.6963	4.1286	0.0199	0.7278	-1.5117	-0.266	0.3566	-0.3618	0.6306	0.8556	-0.0823	0.7175	0.1491	-0.1475	0.1793	-0.0793	0.7521	48.7281	53.6463	48.74
19	3.3666	1.248	-3.934	5.7852	-2.2786	6.1771	-0.0426	0.7772	1.0319	0.2806	0.6367	1.0689	-0.9274	0.3073	-0.436	0.6194	0.045	0.0927	0.3978	0.0938	0.7977	48.0263	62.0874	45.3037
20	2.9912	1.4152	0.863	4.1947	3.6106	5.2826	0.1725	-0.4345	1.0932	1.1717	-0.257	1.488	-0.0076	0.1786	0.1577	0.718	-0.0977	-0.1071	0.4808	0.0999	0.8846	44.4497	62.8855	57.9276
21	3.983	4.7427	5.2411	5.7307	6.6846	7.3945	1.7465	-1.2661	-1.9236	1.957	-0.9223	-2.5445	0.987	-0.1222	-0.6125	0.9687	-0.2683	-0.1208	0.7898	0.0917	1.0029	47.9425	57.0592	62.9586
22	8.4641	2.2884	-0.8166	3.8374	-0.8102	4.6133	0.887	-1.0421	-0.3171	0.4229	-0.3594	-0.3338	0.2509	0.3565	-0.5281	0.7012	0.1676	0.0466	0.495	-0.0149	0.5196	35.8055	70.5284	58.0815
23	0.2545	1.1972	0.1516	8.6212	2.2405	3.1852	0.515	0.4357	1.7714	2.3272	-1.8883	-0.6628	0.5485	0.7219	1.5225	1.2137	-0.5729	-0.0485	1.3547	0.3248	1.8361	54.854	85.085	54.2582
24	3.7341	0.1201	-1.9938	5.1067	2.035	6.3914	1.4599	1.1523	0.1697	1.8146	-0.5989	-0.0456	0.5519	-0.1723	0.2382	0.4967	-0.0483	0.042	0.4327	0.1253	1.0826	41.3966	69.1354	49.2121
25	4.9979	3.5561	-2.1495	6.7478	-0.5518	4.5025	0.1215	-0.3393	1.2921	-0.3971	-0.3468	0.7517	-0.4391	0.1283	0.1385	0.4172	0.0749	0.018	0.3502	-0.0469	0.86	30.0926	80.4385	52.5398
26	4.5029	0.1155	0.4256	2.8508	0.8152	1.8382	-1.0725	1.566	-0.0072	-1.0254	0.8855	0.3748	-0.6184	0.3308	0.1493	0.9018	-0.1063	-0.1725	0.7339	0.0566	0.4176	47.4785	61.593	26.6172
27	0.0852	0.5939	0.3009	5.7762	1.1373	1.1781	0.0396	0.2107	0.9609	-0.1353	-0.2151	0.7894	-0.136	-0.3849	0.1933	0.5621	0.072	-0.0119	0.6433	-0.0191	0.6016	47.8837	59.3926	35.9527
28	4.7773	1.0079	1.3382	4.3748	1.6858	1.1047	-0.3102	-0.1165	-1.1595	-0.5011	-0.2028	-0.6525	0.8012	-0.0864	0.0158	0.4854	0.058	-0.0976	0.7317	-0.0589	1.0558	54.6872	49.5016	30.8637

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 36 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 37 through 71 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 72 through 105 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 106 through 137 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 6 through 34 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 35 through 46 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 47 through 100 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 101 through 105 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 106 through 137 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 6 through 46 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 47 through 136 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 7 through 33 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 34 through 105 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 106 through 135 )
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 7 through 71 )
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 72 through 105 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 106 through 136 )
18	X-RAY DIFFRACTION	18	chain 'F' and (resid 6 through 36 )
19	X-RAY DIFFRACTION	19	chain 'F' and (resid 37 through 71 )
20	X-RAY DIFFRACTION	20	chain 'F' and (resid 72 through 105 )
21	X-RAY DIFFRACTION	21	chain 'F' and (resid 106 through 136 )
22	X-RAY DIFFRACTION	22	chain 'G' and (resid 6 through 36 )
23	X-RAY DIFFRACTION	23	chain 'G' and (resid 37 through 42 )
24	X-RAY DIFFRACTION	24	chain 'G' and (resid 43 through 66 )
25	X-RAY DIFFRACTION	25	chain 'G' and (resid 67 through 136 )
26	X-RAY DIFFRACTION	26	chain 'H' and (resid 6 through 41 )
27	X-RAY DIFFRACTION	27	chain 'H' and (resid 42 through 105 )
28	X-RAY DIFFRACTION	28	chain 'H' and (resid 106 through 136 )

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