PDB-4owt: Structural basis of SOSS1 complex assembly

ID or keywords:

Entry

Database: PDB / ID: 4owt

Title

Structural basis of SOSS1 complex assembly

Components

Integrator complex subunit 3
SOSS complex subunit B1Southern Okanagan Secondary School
SOSS complex subunit CSouthern Okanagan Secondary School

Keywords

DNA BINDING PROTEIN / SOSS1 complex / DNA double-strand breaks /

homologous recombination / ssDNA- binding protein

Function / homology

Function and homology information

SOSS complex / snRNA processing /

integrator complex / establishment of protein localization to telomere / regulation of transcription elongation by RNA polymerase II / G-rich strand telomeric DNA binding / mitotic G2/M transition checkpoint / response to ionizing radiation / positive regulation of telomere capping / RNA polymerase II transcribes snRNA genes ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2 Å

Authors

Ren, W. / Sun, Q. / Tang, X. / Song, H.

Funding support

China,

Singapore, 4items

Organization	Grant number	Country
National Natural Science Foundation of China (NSFC)	31270816	China
the Agency for Science, Technology and Research		Singapore
National Basic Research Program of China (973 Program)	2012CB944402	China
National Basic Research Program of China (973 Program)	2013CB911003	China

Citation

Journal: Cell Rep / Year: 2014
Title: Structural Basis of SOSS1 Complex Assembly and Recognition of ssDNA.
Authors: Ren, W. / Chen, H. / Sun, Q. / Tang, X. / Lim, S.C. / Huang, J. / Song, H.

History

Deposition	Feb 3, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 16, 2014	Provider: repository / Type: Initial release
Revision 1.1	Sep 6, 2017	Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Derived calculations / Other / Source and taxonomy / Structure summary Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_symm_contact / struct_keywords Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2 / _struct_keywords.text
Revision 1.2	Jan 8, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Dec 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4owt.cif.gz	262.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4owt.ent.gz	208.2 KB	Display	PDB format
PDBx/mmJSON format	4owt.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ow/4owt ftp://data.pdbj.org/pub/pdb/validation_reports/ow/4owt	HTTPS FTP

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Related structure data

Related structure data	4owwC 4owxC C: citing same article (ref.)
Similar structure data	6axf-4 6axf-1 5bxr-1 23566 4y97-3 6rhe-d 5bxt-1 6o2a-4 2ct8-1 5k94-2 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	#67 - Jul 2005 TATA-Binding Protein similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #227 - Nov 2018 Telomerase similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1)

Deposited unit

A: Integrator complex subunit 3

B: SOSS complex subunit B1

C: SOSS complex subunit C

88 kDa, 3 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)	116.809, 116.809, 109.832
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	Integrator complex subunit 3 / / Int3 / SOSS complex subunit A / Sensor of single-strand DNA complex subunit A / Sensor of ssDNA subunit A Mass: 54147.645 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INTS3, C1orf193, C1orf60 / Production host: Escherichia coli (E. coli) / References: UniProt: Q68E01
#2: Protein	SOSS complex subunit B1 / Southern Okanagan Secondary School / Nucleic acid-binding protein 2 / Oligonucleotide/oligosaccharide-binding fold-containing protein 2B ...Nucleic acid-binding protein 2 / Oligonucleotide/oligosaccharide-binding fold-containing protein 2B / Sensor of single-strand DNA complex subunit B1 / Sensor of ssDNA subunit B1 / SOSS-B1 / Single-stranded DNA-binding protein 1 / hSSB1 Mass: 22364.873 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NABP2, OBFC2B, SSB1, LP3587 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BQ15
#3: Protein	SOSS complex subunit C / Southern Okanagan Secondary School / INTS3- and NABP-interacting protein / Sensor of single-strand DNA complex subunit C / Sensor of ...INTS3- and NABP-interacting protein / Sensor of single-strand DNA complex subunit C / Sensor of ssDNA subunit C / SOSS-C / Single-stranded DNA-binding protein-interacting protein 1 / hSSBIP1 Mass: 11441.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INIP, C9orf80, SSBIP1, HSPC043, HSPC291 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NRY2
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 410 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.49 Å³/Da / Density % sol: 50.64 %
Crystal grow	Temperature: 289.15 K / Method: vapor diffusion, hanging drop Details: 21% PEG2000 MME, 0.1M MES pH6.0, 0.05M sodium chloride

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 1, 2013
Radiation	Protocol: MAD / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793 Å / Relative weight: 1
Reflection	Resolution: 2→20 Å / Num. obs: 58840 / % possible obs: 100 % / Redundancy: 11.9 % / Net I/σ(I): 9.9

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Processing

Software

Name: PHENIX / Version: (PHENIX.REFINE: 1.8.1_1168) / Classification: refinement

Refinement

Method to determine structure:

MAD / Resolution: 2→19.9 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0.86 / Phase error: 19.89 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.195	5723	5.06 %	Random selection
R_work	0.172	-	-	-
obs	0.173	113174	100 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2→19.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4603	0	0	410	5013

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	4696
X-RAY DIFFRACTION	f_angle_d	0.993	6355
X-RAY DIFFRACTION	f_dihedral_angle_d	14.403	1750
X-RAY DIFFRACTION	f_chiral_restr	0.064	741
X-RAY DIFFRACTION	f_plane_restr	0.004	799

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 (%)
2-2.0227	0.3323	185	0.3146	3614	X-RAY DIFFRACTION	100
2.0227-2.0465	0.3151	177	0.2932	3601	X-RAY DIFFRACTION	100
2.0465-2.0714	0.2873	175	0.2746	3589	X-RAY DIFFRACTION	100
2.0714-2.0976	0.2867	172	0.2599	3549	X-RAY DIFFRACTION	100
2.0976-2.1252	0.2646	176	0.2486	3617	X-RAY DIFFRACTION	100
2.1252-2.1543	0.2487	195	0.2266	3586	X-RAY DIFFRACTION	100
2.1543-2.185	0.2585	182	0.2267	3582	X-RAY DIFFRACTION	100
2.185-2.2176	0.234	202	0.2244	3591	X-RAY DIFFRACTION	100
2.2176-2.2522	0.2304	181	0.2103	3584	X-RAY DIFFRACTION	100
2.2522-2.289	0.2355	230	0.2001	3571	X-RAY DIFFRACTION	100
2.289-2.3285	0.2086	180	0.1899	3599	X-RAY DIFFRACTION	100
2.3285-2.3707	0.1944	207	0.1809	3536	X-RAY DIFFRACTION	100
2.3707-2.4163	0.2054	182	0.1802	3577	X-RAY DIFFRACTION	100
2.4163-2.4655	0.2019	210	0.1752	3587	X-RAY DIFFRACTION	100
2.4655-2.519	0.2572	179	0.1783	3542	X-RAY DIFFRACTION	100
2.519-2.5775	0.2	165	0.1628	3622	X-RAY DIFFRACTION	100
2.5775-2.6418	0.2019	188	0.1662	3594	X-RAY DIFFRACTION	100
2.6418-2.713	0.2212	207	0.1625	3616	X-RAY DIFFRACTION	100
2.713-2.7927	0.1957	188	0.1634	3533	X-RAY DIFFRACTION	100
2.7927-2.8826	0.1945	196	0.1596	3576	X-RAY DIFFRACTION	100
2.8826-2.9853	0.1902	207	0.1565	3589	X-RAY DIFFRACTION	100
2.9853-3.1044	0.2018	163	0.161	3593	X-RAY DIFFRACTION	100
3.1044-3.2451	0.2029	197	0.1552	3594	X-RAY DIFFRACTION	100
3.2451-3.4153	0.1582	188	0.1543	3581	X-RAY DIFFRACTION	100
3.4153-3.6281	0.1829	184	0.1508	3548	X-RAY DIFFRACTION	100
3.6281-3.9063	0.1706	215	0.1384	3606	X-RAY DIFFRACTION	100
3.9063-4.2958	0.1571	200	0.1385	3547	X-RAY DIFFRACTION	100
4.2958-4.9093	0.1491	193	0.14	3583	X-RAY DIFFRACTION	100
4.9093-6.1546	0.189	203	0.1819	3585	X-RAY DIFFRACTION	100
6.1546-19.8981	0.1877	196	0.1815	3559	X-RAY DIFFRACTION	100

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	0.8137	-0.1208	0.5681	1.1021	-0.21	4.8757	-0.1872	-0.1254	-0.0914	-0.168	-0.4249	-0.6304	0.2178	0.9776	0.4778	0.3844	0.0728	0.2032	0.5569	0.0214	0.5573	40.5297	76.9984	9.8485
2	3.9614	-0.6432	0.1296	4.1635	1.7993	4.0792	0.1037	0.7033	-0.06	-1.078	-0.2392	0.1568	-0.3939	-0.1396	0.2425	0.4766	-0.0278	0.1574	0.3496	-0.0746	0.334	33.4241	78.8429	-4.5875
3	2.823	0.4932	0.0484	2.6693	0.7392	3.5187	-0.2024	0.0336	0.0361	-0.4609	0.0568	-0.116	0.2412	-0.0981	0.1445	0.3438	0.0204	0.176	0.2423	-0.0371	0.3214	27.84	80.7917	6.2167
4	1.9482	-0.2596	0.3185	1.6112	-0.7476	2.7917	-0.0313	-0.1594	0.0503	0.0439	0.1043	0.0749	-0.1015	-0.1541	-0.0353	0.3	-0.0042	0.133	0.1883	-0.0619	0.2782	22.9683	85.0521	12.4664
5	2.4826	0.1459	-0.1967	1.6322	-0.0814	2.5075	-0.0193	0.0945	0.168	-0.2207	0.0556	-0.1295	0.0649	0.0439	-0.0545	0.2271	-0.0019	0.1102	0.1427	-0.0303	0.2091	15.9383	89.0134	21.844
6	1.1748	0.5326	-1.1653	2.4692	-0.9281	1.914	-0.0219	0.1762	0.0256	-0.2923	0.153	0.0329	0.117	-0.2945	-0.1475	0.1952	-0.0233	0.0132	0.1834	-0.025	0.1301	2.1063	88.7354	28.0261
7	2.1611	-0.7489	-0.1762	1.6496	-0.2977	2.3765	-0.0696	-0.1437	-0.2194	-0.1022	0.0051	-0.3661	0.2615	0.4382	0.0347	0.1935	0.0465	0.0799	0.2525	0.0092	0.2705	20.7205	72.1437	38.0641
8	2.0785	-0.2609	-0.0779	2.1247	-0.4997	2.2791	-0.0505	-0.2242	-0.1141	-0.0496	0.0482	-0.0492	0.3247	-0.0739	-0.0055	0.2006	-0.044	0.0593	0.2124	-0.002	0.1487	3.0571	71.1862	45.8118
9	1.4217	-0.2709	-0.0249	1.762	2.0638	4.8413	0.0042	-0.1258	-0.0849	0.1419	-0.0557	0.1051	0.3462	-0.2384	0.0683	0.2508	-0.041	0.0535	0.311	0.0581	0.1955	1.5333	67.409	57.1749
10	0.8256	-0.6594	-0.32	0.6268	0.3754	0.2503	-0.0578	-0.1226	-0.7744	0.1404	0.1382	-0.0541	0.4057	0.5197	-0.1894	0.3707	0.3473	0.2519	0.9172	0.3616	1.094	45.6805	58.1793	34.7735
11	3.6171	0.3156	1.6136	4.6579	-2.6827	7.7599	-0.3717	-0.5	-0.6539	0.9015	-0.6323	-1.3008	-0.9302	1.5964	0.8189	0.4247	0.0925	-0.1118	0.9652	0.2272	0.8082	46.3176	70.4152	36.9132
12	3.6492	-1.2337	1.3081	0.8291	-0.3884	0.4667	-0.0869	-0.198	-0.4317	0.1028	-0.2598	-0.9653	0.3465	1.1267	0.0563	0.3417	0.1912	0.029	1.2467	0.2343	1.0001	48.6799	67.2813	31.5672
13	0.1565	-0.1752	0.2311	0.8301	-0.1324	0.4297	-0.1649	-0.6533	-0.6738	0.5073	0.005	-0.8505	0.1964	0.3672	0.0636	0.2584	0.3809	0.0789	0.6487	0.3785	0.9963	39.4113	61.6184	40.6533
14	7.6712	2.1856	-2.0337	5.1558	-0.6547	8.1745	-0.0492	-0.9581	-0.1318	1.7445	-0.1907	-0.5527	0.3704	0.1889	0.1474	0.5829	0.039	-0.1042	0.2365	-0.0646	0.2849	10.7898	94.566	52.9929
15	2.1459	0.1877	0.7849	3.5228	-1.3821	4.6925	-0.0171	-0.2387	0.1581	0.4886	-0.0265	0.0954	-0.3386	-0.1723	0.0374	0.1553	-0.0038	0.0272	0.1749	-0.0569	0.132	4.4842	87.9547	48.1145

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 33 THROUGH 63 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 64 THROUGH 99 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 100 THROUGH 136 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 137 THROUGH 170 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 171 THROUGH 222 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 223 THROUGH 297 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 298 THROUGH 395 )
8	X-RAY DIFFRACTION	8	CHAIN 'A' AND (RESID 396 THROUGH 465 )
9	X-RAY DIFFRACTION	9	CHAIN 'A' AND (RESID 466 THROUGH 498 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 6 THROUGH 22 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 23 THROUGH 69 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 70 THROUGH 97 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 98 THROUGH 109 )
14	X-RAY DIFFRACTION	14	CHAIN 'C' AND (RESID 63 THROUGH 78 )
15	X-RAY DIFFRACTION	15	CHAIN 'C' AND (RESID 79 THROUGH 101 )

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