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- PDB-4owx: Structural basis of SOSS1 in complex with a 12nt ssDNA -

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Basic information

Entry
Database: PDB / ID: 4owx
TitleStructural basis of SOSS1 in complex with a 12nt ssDNA
Components
  • DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
  • Integrator complex subunit 3
  • SOSS complex subunit B1Southern Okanagan Secondary School
KeywordsDNA BINDING PROTEIN/DNA / SOSS1 complex / DNA double-strand breaks / homologous recombination / ssDNA- binding protein / DNA BINDING PROTEIN-DNA complex
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 ...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 / DNA polymerase binding / double-strand break repair via homologous recombination / single-stranded DNA binding / site of double-strand break / chromosome, telomeric region / DNA repair / DNA damage response / DNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Integrator complex subunit 3, N-terminal / Integrator complex subunit 3 / Integrator complex subunit 3 N-terminal / : / Single-stranded DNA binding protein Ssb-like, OB fold / OB-fold nucleic acid binding domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Integrator complex subunit 3 / SOSS complex subunit B1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsRen, W. / Sun, Q. / Tang, X. / Song, H.
Funding support Singapore, China, 2items
OrganizationGrant numberCountry
the Agency for Science, Technology and Research Singapore
National Natural Science Foundation of China (NSFC)31270816 China
CitationJournal: 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
DepositionFeb 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_entity_src_syn / pdbx_struct_oper_list
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_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
A: Integrator complex subunit 3
B: SOSS complex subunit B1


Theoretical massNumber of molelcules
Total (without water)82,0333
Polymers82,0333
Non-polymers00
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-24 kcal/mol
Surface area26760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.630, 162.520, 65.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: DNA chain DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')


Mass: 3605.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Protein Integrator complex subunit 3 / / Int3 / SOSS complex subunit A / Sensor of single-strand DNA complex subunit A / Sensor of ssDNA subunit A


Mass: 56063.215 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
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.7 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 16% PEG3350, 0.1M MES pH6.0, 0.1M ammonium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→41.81 Å / Num. obs: 47747 / % possible obs: 99.8 % / Redundancy: 7.78 % / Net I/σ(I): 11.4

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.1_1168) / Classification: refinement
RefinementResolution: 2.3→41.807 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2258 2413 5.06 %Random selection
Rwork0.1824 ---
obs0.1846 47686 99.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→41.807 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4555 180 0 171 4906
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084840
X-RAY DIFFRACTIONf_angle_d1.1196584
X-RAY DIFFRACTIONf_dihedral_angle_d16.5331833
X-RAY DIFFRACTIONf_chiral_restr0.075763
X-RAY DIFFRACTIONf_plane_restr0.004802
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.3470.30411570.27492645X-RAY DIFFRACTION100
2.347-2.3980.30631450.26222603X-RAY DIFFRACTION100
2.398-2.45380.31091460.24722617X-RAY DIFFRACTION100
2.4538-2.51510.26131350.23672648X-RAY DIFFRACTION100
2.5151-2.58310.26551500.21622634X-RAY DIFFRACTION100
2.5831-2.65910.2491460.20522628X-RAY DIFFRACTION100
2.6591-2.74490.2141250.19752648X-RAY DIFFRACTION100
2.7449-2.8430.29361290.20122652X-RAY DIFFRACTION100
2.843-2.95680.2531320.19012641X-RAY DIFFRACTION100
2.9568-3.09130.25191380.19552673X-RAY DIFFRACTION100
3.0913-3.25430.28471530.19142636X-RAY DIFFRACTION100
3.2543-3.45810.22821390.18242682X-RAY DIFFRACTION100
3.4581-3.72490.21191420.17272669X-RAY DIFFRACTION100
3.7249-4.09950.19131390.15642692X-RAY DIFFRACTION100
4.0995-4.6920.16821390.14872707X-RAY DIFFRACTION100
4.692-5.90870.2161420.17632719X-RAY DIFFRACTION100
5.9087-41.81410.22941560.18382779X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
16.23630.2996-1.76099.9208-1.80738.2657-0.16560.5414-0.3164-0.61820.4529-0.0462-0.3827-1.5334-0.29940.43250.03310.03930.81220.11370.5822-25.165653.620533.0646
25.18911.1552-1.69741.981-2.80383.33570.16010.68760.4595-0.2296-0.1395-0.2099-0.77160.2098-0.02090.67120.0187-0.02820.53980.07080.40882.304447.67823.613
32.505-1.57490.36135.5848-0.8082.74540.24610.3465-0.4092-0.861-0.2484-0.25540.16840.22520.00980.370.00070.02110.3545-0.03890.34279.888621.00411.87
44.508-0.46820.33253.78340.51312.9087-0.0006-0.9308-0.89690.70830.1255-0.23530.5417-0.0919-0.06370.4172-0.012-0.07310.5020.29750.512311.310816.597541.4271
52.20850.0769-0.87253.51413.25683.54030.2495-1.02861.1180.27750.0934-0.5461-1.17940.4228-0.38550.60210.0145-0.0330.6325-0.09660.5993-2.131354.248343.3174
69.2199-3.2374-0.7197.99942.99474.114-0.3059-1.06370.85980.26740.28130.0288-0.76840.4094-0.10070.531-0.03880.03410.4431-0.1790.456-9.734459.322540.3458
78.0266-0.57044.19932.04330.6792.85750.1002-1.201-0.55570.6778-0.03320.1080.05770.0461-0.3590.33480.00930.05840.53370.04330.2706-7.139243.167737.6822
85.3011-0.5852.82144.75352.67599.03790.2729-1.3021-1.89020.68130.99591.20930.6814-0.7861-0.74220.3999-0.1292-0.04410.77910.38551.13-24.777139.761837.294
95.225-1.65923.72812.3262-1.66654.4045-0.4704-0.6853-0.11320.18750.51190.4204-0.3162-0.3871-0.49190.28780.03810.07090.51420.06850.4539-16.377746.039638.1433
105.2031-3.8214-6.09812.85894.54097.2153-0.05260.6779-0.5931-0.26040.06081.36260.327-1.4488-0.13390.4216-0.0413-0.11660.57530.02490.6094-18.374642.548627.9816
114.6296-1.1037-0.79125.40530.00992.8128-0.0817-0.41390.14210.3830.17970.2779-0.2265-0.34650.02380.26320.0421-0.00070.4927-0.00250.2558-12.886849.674137.7697
122.6231.2637-1.6662.441.48773.98180.30221.05770.5292-1.0634-0.27610.0416-0.30940.19830.04710.27070.02510.00570.42610.07320.3545-8.949349.331128.4523
132.536-0.6599-0.08541.93750.41730.9681-0.2519-0.91460.15120.52210.36420.1812-0.183-0.14660.06190.43270.1115-0.00480.84990.03250.2873-4.504143.230245.1798
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 1 through 9 )
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 82 )
3X-RAY DIFFRACTION3chain 'A' and (resid 83 through 297 )
4X-RAY DIFFRACTION4chain 'A' and (resid 298 through 497 )
5X-RAY DIFFRACTION5chain 'B' and (resid 5 through 9 )
6X-RAY DIFFRACTION6chain 'B' and (resid 10 through 18 )
7X-RAY DIFFRACTION7chain 'B' and (resid 19 through 26 )
8X-RAY DIFFRACTION8chain 'B' and (resid 27 through 31 )
9X-RAY DIFFRACTION9chain 'B' and (resid 32 through 55 )
10X-RAY DIFFRACTION10chain 'B' and (resid 56 through 61 )
11X-RAY DIFFRACTION11chain 'B' and (resid 62 through 86 )
12X-RAY DIFFRACTION12chain 'B' and (resid 87 through 97 )
13X-RAY DIFFRACTION13chain 'B' and (resid 98 through 111 )

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