SAXSdb — 4oww

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

Integrator complex subunit 3

Homo sapiens

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 × 3 DNA 1 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 1–500	Not recorded	;DNA (5'-D(PTPTPTPTPTPT)-3') ; × 1 SOSS complex subunit B1 × 1 （Q9BQ15） SOSS complex subunit C × 1 （Q9NRY2）	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

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 4OWW	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
4OWX Structural basis of SOSS1 in complex with a 12nt ssDNA Deposited 2014-02-04	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: trimeric	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；16% PEG3350, 0.1M MES pH6.0, 0.1M ammonium formate	Resolution 2.30 Å R-free 0.226
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 × 3 DNA 1 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain B； UniProt 1–211	Not recorded	;DNA (5'-D(PTPTPTPTPTPT)-3') ; × 1 Integrator complex subunit 3 × 1 （Q68E01） SOSS complex subunit C × 1 （Q9NRY2）	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

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 4OWW	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
4OWX Structural basis of SOSS1 in complex with a 12nt ssDNA Deposited 2014-02-04	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 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 K；16% PEG3350, 0.1M MES pH6.0, 0.1M ammonium formate	Resolution 2.30 Å R-free 0.226
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

SOSS complex subunit C

Homo sapiens

UniProt Q9NRY2

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 × 3 DNA 1 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain C； UniProt 1–104	Not recorded	;DNA (5'-D(PTPTPTPTPTPT)-3') ; × 1 Integrator complex subunit 3 × 1 （Q68E01） SOSS complex subunit B1 × 1 （Q9BQ15）	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

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 4OWW	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 C 1–104（104 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
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 C 1–104（104 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

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SOSSC_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain C； PDBConstruct 1–104； UniProt 1–104

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4oww
Deposition date deposition_date	2014-02-04
Structure title title	Structural basis of SOSS1 in complex with a 35nt ssDNA
Keywords keywords	SOSS1 complex, DNA double-strand breaks, homologous recombination, ssDNA-binding protein, DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	29.35 Å
Radius of gyration Rg (electron density) rg_electron	28.17 Å
Forward intensity I(0) i0	79400400.00
Molecular weight molecular_weight	70936.0 kDa
Excluded volume excluded_volume	89255 Å³
Envelope volume envelope_volume	108610 Å³
Hydration-shell volume shell_volume	32442 Å³
Envelope diameter envelope_diameter	99.1 Å
Shell Rg shell_rg	35.15 Å
Envelope Rg envelope_rg	28.33 Å
Shape Rg shape_rg	28.15 Å
Total Rg total_rg	28.92 Å
Total atoms total_atoms	4971
Residues n_residues	615
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	92.4 Å
Rg (real space) rg_real	29.30 Å
Rg uncertainty (real space) rg_real_error	0.64 Å
I(0) (real space) i0_real	7.9400e+07
I(0) uncertainty (real space) i0_real_error	1.1350e+06
Rg (reciprocal space) rg_reciprocal	29.33 Å
I(0) (reciprocal space) i0_reciprocal	79400000.0000
Solution quality estimate total_estimate	0.9094
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.5 Å
Skewness Skewness skewness	0.233
Kurtosis Kurtosis kurtosis	-0.582
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	21630000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.953; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.962

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(PTPTPTPTPTPT)-3') ;
Molecular weight formula_weight	10601.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	L
Atom count atom_count	5184

TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

Entity 2 Entity 2 polymer

Description description	Integrator complex subunit 3
Molecular weight formula_weight	56063.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MELQKGKGAAAAAAASGAAGGGGGGAGAGAPGGGRLLLSTSLDAKDELEERLERCMSIVTSMTAGVSEREANDALNAYVCKGLPQHEEICLGLFTLILTEPAQAQKCYRDLALVSRDGMNIVLNKINQILMEKYLKLQDTCRTQLVWLVRELVKSGVLGADGVCMTFMKQIAGGDVTAKNIWLAESVLDILTEQREWVLKSSILIAMAVYTYLRLIVDHHGTAQLQALRQKEVDFCISLLRERFMECLMIGRDLVRLLQNVARIPEFELLWKDIIHNPQALSPQFTGILQLLQSRTSRKFLACRLTPDMETKLLFMTSRVRFGQQKRYQDWFQRQYLSTPDSQSLRCDLIRYICGVVHPSNEVLSSDILPRWAIIGWLLTTCTSNVAASNAKLALFYDWLFFSPDKDSIMNIEPAILVMHHSMKPHPAITATLLDFMCRIIPNFYPPLEGHVRQGVFSSLNHIVEKRVLAHLAPLFDNPKLDKELRAMLREKFPEFCSSP

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	SOSS complex subunit B1
Molecular weight formula_weight	22364.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MTTETFVKDIKPGLKNLNLIFIVLETGRVTKTKDGHEVRTCKVADKTGSINISVWDDVGNLIQPGDIIRLTKGYASVFKGCLTLYTGRGGDLQKIGEFCMVYSEVPNFSEPNPEYSTQQAPNKAVQNDSNPSASQPTTGPSAASPASENQNGNGLSAPPGPGGGPHPPHTPSHPPSTRITRSQPNHTPAGPPGPSSNPVSNGKETRRSSKR

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	SOSS complex subunit C
Molecular weight formula_weight	11441.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MAANSSGQGFQNKNRVAILAELDKEKRKLLMQNQSSTNHPGASIALSRPSLNKDFRDHAEQQHIAAQQKAALQHAHAHSSGYFITQDSAFGNLILPVLPRLDPE

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	213

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	4owwB00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

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8. Citations (1)

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Unit-cell length a length_a	82.350 Å
Unit-cell length b length_b	90.970 Å
Unit-cell length c length_c	111.060 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	19.959 Å
R factor r_factor	0.1818
R_work r_work	0.1799
R_free r_free	0.2183

fit	/app/data/saxs_computation/ow/4oww/4oww.fit
pddf	/app/data/pr_computation/ow/4oww/4oww.pr.out
profile	/app/data/saxs_computation/ow/4oww/4oww.dat

Structural basis of SOSS1 in complex with a 35nt ssDNA

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

Integrator complex subunit 3

State in the Current Structure

Other States of the Same Protein in the Database

SOSS complex subunit B1

State in the Current Structure

Other States of the Same Protein in the Database

SOSS complex subunit C

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)