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- PDB-4oww: Structural basis of SOSS1 in complex with a 35nt ssDNA -

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Basic information

Entry
Database: PDB / ID: 4oww
TitleStructural basis of SOSS1 in complex with a 35nt ssDNA
Components
  • DNA (5'-D(P*TP*TP*TP*TP*TP*T)-3')
  • Integrator complex subunit 3
  • SOSS complex subunit B1Southern Okanagan Secondary School
  • SOSS complex subunit CSouthern Okanagan Secondary School
KeywordsDNA 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 ...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
SOSS complex subunit C / SOSS complex subunit C / 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) ...SOSS complex subunit C / SOSS complex subunit C / 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 / SOSS complex subunit C
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 in Singapore 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*T)-3')
A: Integrator complex subunit 3
B: SOSS complex subunit B1
C: SOSS complex subunit C


Theoretical massNumber of molelcules
Total (without water)100,4724
Polymers100,4724
Non-polymers00
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-29 kcal/mol
Surface area27070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.350, 90.970, 111.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 10601.791 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: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.59 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 20% PEG2000 MME, 0.1M MES pH6.0, 0.05M sodium chloride.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 37719 / % possible obs: 99.8 % / Redundancy: 5.78 % / Net I/σ(I): 7.8

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.1_1168) / Classification: refinement
RefinementResolution: 2.3→19.959 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2183 1878 5 %Random selection
Rwork0.1799 ---
obs0.1818 37579 99.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→19.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4851 120 0 213 5184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055078
X-RAY DIFFRACTIONf_angle_d0.9286895
X-RAY DIFFRACTIONf_dihedral_angle_d15.1141908
X-RAY DIFFRACTIONf_chiral_restr0.059797
X-RAY DIFFRACTIONf_plane_restr0.004853
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.36210.27391440.22792715X-RAY DIFFRACTION100
2.3621-2.43150.26811380.22382698X-RAY DIFFRACTION100
2.4315-2.50980.30651530.21182725X-RAY DIFFRACTION100
2.5098-2.59930.26351320.20432698X-RAY DIFFRACTION100
2.5993-2.70320.25681330.1982720X-RAY DIFFRACTION100
2.7032-2.82590.22771290.19752746X-RAY DIFFRACTION100
2.8259-2.97440.23281500.18982707X-RAY DIFFRACTION100
2.9744-3.16010.2431520.19382750X-RAY DIFFRACTION100
3.1601-3.4030.2161510.18272720X-RAY DIFFRACTION100
3.403-3.74340.22161740.16862756X-RAY DIFFRACTION100
3.7434-4.28040.17211500.1492753X-RAY DIFFRACTION100
4.2804-5.37540.16841400.15012795X-RAY DIFFRACTION99
5.3754-19.960.19631320.17432918X-RAY DIFFRACTION99
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)
13.548-0.0403-1.52682.5335-0.49471.9890.157-0.1540.04180.35760.0185-0.1828-0.08180.3763-0.08090.7323-0.2381-0.1150.7311-0.11430.585452.6462120.584339.7334
23.2012-0.9033-2.09370.95050.22091.56520.2476-0.08730.10680.2317-0.0756-0.1668-0.14980.5784-0.11510.3095-0.1404-0.05350.7280.08090.395857.6076104.204414.822
33.60630.7171-2.00594.1783-1.87484.07560.08620.82870.1996-0.6762-0.2474-0.32360.49290.37240.1390.39170.10480.02071.18840.22220.497873.566397.6444-0.1231
41.32650.64830.18430.8901-0.03021.637-0.04240.6690.1862-0.08780.1135-0.20120.1530.80890.32930.1053-0.12430.03440.56960.1970.288546.518997.68490.097
51.62970.44580.98280.42110.04551.9227-0.08680.24160.1724-0.03960.04330.00570.00590.27440.0690.123-0.03290.00950.19680.05490.145525.38592.92634.1572
62.78510.61190.40291.11410.23323.2026-0.0172-0.302-0.00670.1342-0.00630.06850.2565-0.17570.03690.1693-0.03520.01770.15540.02350.103515.708388.217517.0041
71.5613-0.03250.28821.6554-0.04851.9561-0.1483-0.4643-0.02810.3533-0.01410.45670.329-0.8158-0.18430.3385-0.21020.07220.48170.04090.29474.33280.500217.154
82.9191-2.1617-2.65373.11670.48313.85980.0383-0.17570.09960.88520.1067-0.36020.24150.2865-0.00610.3449-0.0183-0.0680.4610.02180.235843.614799.5644.256
91.2254-1.64240.65825.34953.3646.0872-0.0584-0.4681-0.01170.4838-0.4397-0.138-0.03830.3250.07060.3414-0.1865-0.10330.49260.07130.28949.6076106.72146.4753
103.8596-0.3502-0.54553.99120.50261.3809-0.1521-0.1490.35770.0441-0.0538-0.1075-0.2402-0.08440.0470.2032-0.0758-0.03670.2711-0.0060.151139.0151106.427933.7223
110.1861-0.0872-0.71921.71170.63892.83240.2283-0.1281.29540.02850.2076-0.4186-1.0980.44520.27020.798-0.2268-0.15320.57680.09451.085141.027126.575634.1803
122.48521.4447-0.16735.12940.80711.7777-0.2191-0.00430.3987-0.03710.0713-0.0877-0.2224-0.15240.07080.1722-0.1071-0.0310.296-0.02160.190238.1776108.590136.9968
130.60740.3532-0.44121.4338-0.99611.9566-0.03050.24390.6468-0.1194-0.15540.041-0.87280.1181-0.08290.4888-0.1162-0.05560.27460.10020.344542.5743115.256734.0727
145.34172.07764.67371.38841.01615.32890.03280.0730.2327-0.0839-0.1128-0.0283-0.15010.21780.11450.2276-0.0571-0.02910.35040.00910.158343.4834107.136829.8647
153.41591.0718-0.77961.7603-0.49963.33270.0485-0.11920.67460.4868-0.20060.0835-0.4968-0.0792-0.11220.3575-0.208-0.070.3679-0.08690.222244.3238114.155744.6087
162.32051.60792.73713.24362.88663.7798-0.06490.09160.4814-0.1311-0.0228-0.3371-0.46440.62650.13210.2815-0.2008-0.00480.4397-0.00950.324749.7259108.505930.9062
171.12530.61910.5841.1527-0.39342.0286-0.0017-0.43880.42470.0744-0.05220.3318-0.14540.0293-0.040.2109-0.10920.02570.4097-0.04890.183634.2235102.923538.8054
186.7783-1.028-0.89172.5714-0.26891.4952-0.035-0.3791.07590.30140.17520.1325-0.387-0.4989-0.14980.25720.0341-0.03860.44330.1280.5522.6838105.58053.8723
190.67460.6230.6032.25150.35721.8912-0.14360.07510.56740.02480.00890.225-0.1166-0.2550.20110.1084-0.0111-0.05710.23390.05130.24146.447395.91183.7787
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 2 through 7 )
2X-RAY DIFFRACTION2chain 'A' and (resid 35 through 61 )
3X-RAY DIFFRACTION3chain 'A' and (resid 62 through 82 )
4X-RAY DIFFRACTION4chain 'A' and (resid 83 through 222 )
5X-RAY DIFFRACTION5chain 'A' and (resid 223 through 355 )
6X-RAY DIFFRACTION6chain 'A' and (resid 356 through 445 )
7X-RAY DIFFRACTION7chain 'A' and (resid 446 through 497 )
8X-RAY DIFFRACTION8chain 'B' and (resid 5 through 9 )
9X-RAY DIFFRACTION9chain 'B' and (resid 10 through 18 )
10X-RAY DIFFRACTION10chain 'B' and (resid 19 through 26 )
11X-RAY DIFFRACTION11chain 'B' and (resid 27 through 37 )
12X-RAY DIFFRACTION12chain 'B' and (resid 38 through 47 )
13X-RAY DIFFRACTION13chain 'B' and (resid 48 through 61 )
14X-RAY DIFFRACTION14chain 'B' and (resid 62 through 71 )
15X-RAY DIFFRACTION15chain 'B' and (resid 72 through 86 )
16X-RAY DIFFRACTION16chain 'B' and (resid 87 through 97 )
17X-RAY DIFFRACTION17chain 'B' and (resid 98 through 111 )
18X-RAY DIFFRACTION18chain 'C' and (resid 62 through 78 )
19X-RAY DIFFRACTION19chain 'C' and (resid 79 through 100 )

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