SAXSdb — 8hpp

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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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 573–1043 Chain B； UniProt 573–1043	Fragment：C-terminal motif	Sarcoma antigen 1 × 1 （Q9NXZ1）	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

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 8HPP	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 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 construct Different mutation/modification 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
4OWX Structural basis of SOSS1 in complex with a 12nt ssDNA Deposited 2014-02-04	Different construct Different mutation/modification 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 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 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
8RBZ Structure of Integrator-PP2A-SOSS-CTD post-termination complex Deposited 2023-12-05	Different construct Different mutation/modification 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	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–471； UniProt 573–1043 Author chain B； PDBConstruct 1–471； UniProt 573–1043

Sarcoma antigen 1

Homo sapiens

UniProt Q9NXZ1

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 818–904	Not recorded	Integrator complex subunit 3 × 2 （Q68E01）	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

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	SAGE1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 4–90； UniProt 818–904

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	8hpp
Deposition date deposition_date	2022-12-12
最后修订 last_revision	2023-12-20
Structure title title	Crystal structure of human INTS3 with SAGE1
Keywords keywords	Integrator, Cancer-Testis Antigen, Tumorigenesis, TRANSCRIPTION; TRANSCRIPTION
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	35.14 Å
Radius of gyration Rg (electron density) rg_electron	34.32 Å
Forward intensity I(0) i0	157310000.00
Molecular weight molecular_weight	101350.0 kDa
Excluded volume excluded_volume	127300 Å³
Envelope volume envelope_volume	170960 Å³
Hydration-shell volume shell_volume	42554 Å³
Envelope diameter envelope_diameter	120.7 Å
Shell Rg shell_rg	39.58 Å
Envelope Rg envelope_rg	34.98 Å
Shape Rg shape_rg	34.33 Å
Total Rg total_rg	34.69 Å
Total atoms total_atoms	7102
Residues n_residues	875
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	115.0 Å
Rg (real space) rg_real	35.18 Å
Rg uncertainty (real space) rg_real_error	0.87 Å
I(0) (real space) i0_real	1.5730e+08
I(0) uncertainty (real space) i0_real_error	2.7850e+06
Rg (reciprocal space) rg_reciprocal	35.16 Å
I(0) (reciprocal space) i0_reciprocal	157300000.0000
Solution quality estimate total_estimate	0.8849
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	43.5 Å
Skewness Skewness skewness	0.354
Kurtosis Kurtosis kurtosis	-0.361
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	65160000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.907; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.793

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Integrator complex subunit 3
Molecular weight formula_weight	53929.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7102

DQLDESLRDKVLQLQKGSDTEAQCEVMQEIVDQVLEEDFDSEQLSVLASCLQELFKAHFRGEVLPEEITEESLEESVGKPLYLIFRNLCQMQEDNSSFSLLLDLLSELYQKQPKIGYHLLYYLRASKAAAGKMNLYESFAQATQLGDLHTCLMMDMKACQEDDVRLLCHLTPSIYTEFPDETLRSGELLNMIVAVIDSAQLQELVCHVMMGNLVMFRKDSVLNILIQSLDWETFEQYCAWQLFLAHNIPLETIIPILQHLKYKEHPEALSCLLLQLRREKPSEEMVKMVLSRPCHPDDQFTTSILRHWCMKHDELLAEHIKSLLIKNNSLPRKRQSLRSSSSKLAQLTLEQILEHLDNLRLNLTNTKQNFFSQTPILQALQHVQASCDEAHKMKFSDLFSLAEEYEDSSTKPPKSRRKAALSSPRSRKNATQPPNAEEESGSSSASEEEDTKPKPTKRKRKGSSAVGSDSD

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Sarcoma antigen 1
Molecular weight formula_weight	10827.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

PGSAMAKKINDDIKYQLMKEVRRFGQNYERIFILLEEVQGSMKVKRQFVEFTIKEAARFKKVVLIQQLEKALKEIDSHCHLRKVKHMRKR

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 BL21(DE3)

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8. Citations (1)

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Unit-cell length a length_a	260.119 Å
Unit-cell length b length_b	46.241 Å
Unit-cell length c length_c	103.104 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	113.28 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	47.400 Å
R factor r_factor	0.2173
R_work r_work	0.2152
R_free r_free	0.2573

fit	/app/data/saxs_computation/hp/8hpp/8hpp.fit
pddf	/app/data/pr_computation/hp/8hpp/8hpp.pr.out
profile	/app/data/saxs_computation/hp/8hpp/8hpp.dat

Crystal structure of human INTS3 with SAGE1

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

Sarcoma antigen 1

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)