← Back to search
4owx

Structural basis of SOSS1 in complex with a 12nt ssDNA

Method: X-RAY DIFFRACTION Dmax: 92.3 Å Quality: REASONABLE
▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Integrator complex subunit 3

Homo sapiens

UniProt Q68E01

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 2 DNA 1 PDB declaration: trimeric（3） Consistent with all polymer counts Chain A； UniProt 1–500 Not recorded ;DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*T)-3') ; × 1 SOSS complex subunit B1 × 1 （Q9BQ15） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；289 K；16% PEG3350, 0.1M MES pH6.0, 0.1M ammonium formate Resolution 2.30 Å R-free 0.226

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 4OWX Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4OWT Structural basis of SOSS1 complex assembly Deposited 2014-02-03 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 35–498（464 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；21% PEG2000 MME, 0.1M MES pH6.0, 0.05M sodium chloride
Resolution 2.00 Å R-free 0.195
4OWW Structural basis of SOSS1 in complex with a 35nt ssDNA Deposited 2014-02-04 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain A 1–500（500 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；20% PEG2000 MME, 0.1M MES pH6.0, 0.05M sodium chloride.
Resolution 2.30 Å R-free 0.218
6WLG Ints3 C-terminal Domain Deposited 2020-04-20 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 555–977（423 aa）
Chain B 555–977（423 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.2 M Magnesium Acetate, 13% PEG 3350
Resolution 3.11 Å R-free 0.263
7BV7 INTS3 complexed with INTS6 Deposited 2020-04-09 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 559–994（436 aa）
Chain B 559–994（436 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；288 K；1.7 M Ammonium citrate pH 7.0 4% pentaerythritol ethoxylate
Resolution 2.40 Å R-free 0.249
8HPP Crystal structure of human INTS3 with SAGE1 Deposited 2022-12-12 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 573–1043（471 aa） Fragment：C-terminal motif
Chain B 573–1043（471 aa） Fragment：C-terminal motif
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；0.2 M Ammonium sulfate and 25% Ethylene Glycol 3350
Resolution 3.00 Å R-free 0.257
8RBZ Structure of Integrator-PP2A-SOSS-CTD post-termination complex Deposited 2023-12-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 21 PDB declaration: 21-meric
Chain c 1–1042（1042 aa）
Not recorded ZN ZINC ION × 2 MN MANGANESE (II) ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name INT3_HUMAN
Isoform Q68E01-2
PDB entities 2
Chains and sequence ranges Author chain A； PDBConstruct 1–500； UniProt 1–500

SOSS complex subunit B1

Homo sapiens

UniProt Q9BQ15

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Heteromer Protein × 2 DNA 1 PDB declaration: trimeric（3） Consistent with all polymer counts Chain B； UniProt 1–211 Not recorded ;DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*T)-3') ; × 1 Integrator complex subunit 3 × 1 （Q68E01） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；289 K；16% PEG3350, 0.1M MES pH6.0, 0.1M ammonium formate Resolution 2.30 Å R-free 0.226

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 4OWX Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4OWT Structural basis of SOSS1 complex assembly Deposited 2014-02-03 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–211（211 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；21% PEG2000 MME, 0.1M MES pH6.0, 0.05M sodium chloride
Resolution 2.00 Å R-free 0.195
4OWW Structural basis of SOSS1 in complex with a 35nt ssDNA Deposited 2014-02-04 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain B 1–211（211 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；20% PEG2000 MME, 0.1M MES pH6.0, 0.05M sodium chloride.
Resolution 2.30 Å R-free 0.218
5D8E crystal structure of SSB from homo sapiens Deposited 2015-08-17 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–109（109 aa） Fragment：UNP residues 1-109
Chain D 1–109（109 aa） Fragment：UNP residues 1-109
Mutation：L70M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：L70M Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1M MES pH 6.0, 16% Jeffamine M-600
Resolution 3.00 Å R-free 0.289
5D8E crystal structure of SSB from homo sapiens Deposited 2015-08-17 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 1–109（109 aa） Fragment：UNP residues 1-109
Chain C 1–109（109 aa） Fragment：UNP residues 1-109
Mutation：L70M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：L70M Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1M MES pH 6.0, 16% Jeffamine M-600
Resolution 3.00 Å R-free 0.289
5D8F crystal structure of SSB and ssDNA complex from homo sapiens Deposited 2015-08-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: trimeric
Chain A 1–109（109 aa） Fragment：UNP residues 1-109
Chain B 1–109（109 aa） Fragment：UNP residues 1-109
Not recorded PEG DI(HYDROXYETHYL)ETHER × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1M MES pH 6.0, 16% Jeffamine M-600
Resolution 2.35 Å R-free 0.282
8RBZ Structure of Integrator-PP2A-SOSS-CTD post-termination complex Deposited 2023-12-05 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 21 PDB declaration: 21-meric
Chain B 1–211（211 aa）
Not recorded ZN ZINC ION × 2 MN MANGANESE (II) ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SOSB1_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain B； PDBConstruct 1–211； UniProt 1–211

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 4owx

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4owx
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id4owx
Deposition date deposition_date2014-02-04
Structure title titleStructural basis of SOSS1 in complex with a 12nt ssDNA
Keywords keywordsSOSS1 complex, DNA double-strand breaks, homologous recombination, ssDNA- binding protein, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/DNA
Experimental Method methodX-RAY DIFFRACTION
▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier29.53 Å
Radius of gyration Rg (electron density) rg_electron28.26 Å
Forward intensity I(0) i073553800.00
Molecular weight molecular_weight67687.0 kDa
Excluded volume excluded_volume84967 ų
Envelope volume envelope_volume105310 ų
Hydration-shell volume shell_volume31429 ų
Envelope diameter envelope_diameter98.3 Å
Shell Rg shell_rg35.11 Å
Envelope Rg envelope_rg28.48 Å
Shape Rg shape_rg28.23 Å
Total Rg total_rg29.03 Å
Total atoms total_atoms4735
Residues n_residues580
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax92.3 Å
Rg (real space) rg_real29.49 Å
Rg uncertainty (real space) rg_real_error0.55 Å
I(0) (real space) i0_real7.3550e+07
I(0) uncertainty (real space) i0_real_error9.4920e+05
Rg (reciprocal space) rg_reciprocal29.51 Å
I(0) (reciprocal space) i0_reciprocal73550000.0000
Solution quality estimate total_estimate0.7300
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary32.5 Å
Skewness Skewness skewness0.223
Kurtosis Kurtosis kurtosis-0.594
Angular range angular_range— – 0.2700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha23180000.0000
Real-space data points n_real_points55
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.960; Stabil: 1.000; Sysdev: 0.218; Positv: 1.000; Valcen: 0.994; Smooth: 0.957
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

▼

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id4owxB00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily140 — Nucleic acid-binding proteins
▶

8. Citations (1)

▶

9. Files and Curves (10)