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9ep4

Structure of Integrator subcomplex INTS5/8/15

Method: ELECTRON MICROSCOPY Dmax: 220.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Integrator complex subunit 8

Homo sapiens

UniProt Q75QN2

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 1–995 Not recorded Integrator complex subunit 5 × 1 （Q6P9B9） Integrator complex subunit 15 × 1 （Q96N11） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.20 Å

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 9EP4 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7CUN The structure of human Integrator-PP2A complex Deposited 2020-08-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain H 1–995（995 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 3.50 Å
7PKS Structural basis of Integrator-mediated transcription regulation Deposited 2021-08-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 31-meric
Chain h 1–995（995 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 10 MN MANGANESE (II) ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7YCX The structure of INTAC-PEC complex Deposited 2022-07-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain H 1–995（995 aa）
Not recorded ZN ZINC ION × 10 MN MANGANESE (II) ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.18 Å
8RBX Structure of Integrator-PP2A bound to a paused RNA polymerase II-DSIF-NELF-nucleosome complex Deposited 2023-12-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 43 PDB declaration: 46-meric
Chain h 1–995（995 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 MN MANGANESE (II) ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8RBZ Structure of Integrator-PP2A-SOSS-CTD post-termination complex Deposited 2023-12-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 21 PDB declaration: 21-meric
Chain h 1–995（995 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
8RC4 Structure of Integrator-PP2A complex Deposited 2023-12-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: 16-meric
Chain h 1–995（995 aa）
Not recorded MN MANGANESE (II) ION × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8YJB Cryo-EM structure of the human DSS1-INTAC complex Deposited 2024-03-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain H 1–995（995 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 4.10 Å
9EOF Structure of the human INTS5/8/10/15 subcomplex Deposited 2024-03-14 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 1–995（995 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.70 Å
9VD9 Cryo-EM structure of the human DSS1-INTAC-PEC complex Deposited 2025-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 35 PDB declaration: 38-meric
Chain H 1–995（995 aa）
Not recorded ZN ZINC ION × 10 MN MANGANESE (II) ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name INT8_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–995； UniProt 1–995

Integrator complex subunit 5

Homo sapiens

UniProt Q6P9B9

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 B； UniProt 1–1019 Not recorded Integrator complex subunit 8 × 1 （Q75QN2） Integrator complex subunit 15 × 1 （Q96N11） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.20 Å

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 9EP4 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7CUN The structure of human Integrator-PP2A complex Deposited 2020-08-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain E 1–1019（1019 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 3.50 Å
7PKS Structural basis of Integrator-mediated transcription regulation Deposited 2021-08-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 31-meric
Chain e 1–1019（1019 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 10 MN MANGANESE (II) ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7YCX The structure of INTAC-PEC complex Deposited 2022-07-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain E 1–1019（1019 aa）
Not recorded ZN ZINC ION × 10 MN MANGANESE (II) ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.18 Å
8RBX Structure of Integrator-PP2A bound to a paused RNA polymerase II-DSIF-NELF-nucleosome complex Deposited 2023-12-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 43 PDB declaration: 46-meric
Chain e 1–1019（1019 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 MN MANGANESE (II) ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8RBZ Structure of Integrator-PP2A-SOSS-CTD post-termination complex Deposited 2023-12-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 21 PDB declaration: 21-meric
Chain e 1–1019（1019 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
8RC4 Structure of Integrator-PP2A complex Deposited 2023-12-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: 16-meric
Chain e 1–1019（1019 aa）
Not recorded MN MANGANESE (II) ION × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8YJB Cryo-EM structure of the human DSS1-INTAC complex Deposited 2024-03-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain E 1–1019（1019 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 4.10 Å
9EOF Structure of the human INTS5/8/10/15 subcomplex Deposited 2024-03-14 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain G 1–1019（1019 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.70 Å
9VD9 Cryo-EM structure of the human DSS1-INTAC-PEC complex Deposited 2025-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 35 PDB declaration: 38-meric
Chain E 1–1019（1019 aa）
Not recorded ZN ZINC ION × 10 MN MANGANESE (II) ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name INT5_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–1019； UniProt 1–1019

Integrator complex subunit 15

Homo sapiens

UniProt Q96N11

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 D； UniProt 1–449 Not recorded Integrator complex subunit 8 × 1 （Q75QN2） Integrator complex subunit 5 × 1 （Q6P9B9） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.20 Å

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 9EP4 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8RBX Structure of Integrator-PP2A bound to a paused RNA polymerase II-DSIF-NELF-nucleosome complex Deposited 2023-12-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 43 PDB declaration: 46-meric
Chain o 1–449（449 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 MN MANGANESE (II) ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8RBZ Structure of Integrator-PP2A-SOSS-CTD post-termination complex Deposited 2023-12-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 21 PDB declaration: 21-meric
Chain o 1–449（449 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
8RC4 Structure of Integrator-PP2A complex Deposited 2023-12-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: 16-meric
Chain o 1–449（449 aa）
Not recorded MN MANGANESE (II) ION × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9EOF Structure of the human INTS5/8/10/15 subcomplex Deposited 2024-03-14 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–449（449 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.70 Å
9EP1 Structure of the Integrator arm module containing INTS10/13/14/15 subunits (state 2) Deposited 2024-03-16 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–391（391 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
9FA4 Structure of the Integrator arm module containing subunits INTS10/13/14/15 (state 1) Deposited 2024-05-10 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–449（449 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
9FA7 Structure of the Integrator arm module containing subunits INTS10/13/14/15 (state 3) Deposited 2024-05-10 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–449（449 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name INT15_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain D； PDBConstruct 1–449； UniProt 1–449

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 9ep4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9ep4
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9ep4
Deposition date deposition_date2024-03-17
Structure title titleStructure of Integrator subcomplex INTS5/8/15
Keywords keywordsRNA polymerase II transcription termination, Integrator complex assembly, transcription factors, TRANSCRIPTION; TRANSCRIPTION
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier64.91 Å
Radius of gyration Rg (electron density) rg_electron66.95 Å
Forward intensity I(0) i0664589000.00
Molecular weight molecular_weight218630.0 kDa
Excluded volume excluded_volume275200 ų
Envelope volume envelope_volume448910 ų
Hydration-shell volume shell_volume63728 ų
Envelope diameter envelope_diameter240.7 Å
Shell Rg shell_rg54.02 Å
Envelope Rg envelope_rg66.94 Å
Shape Rg shape_rg66.93 Å
Total Rg total_rg66.69 Å
Total atoms total_atoms15393
Residues n_residues2064
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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax220.6 Å
Rg (real space) rg_real66.44 Å
Rg uncertainty (real space) rg_real_error2.49 Å
I(0) (real space) i0_real6.6430e+08
I(0) uncertainty (real space) i0_real_error1.5960e+07
Rg (reciprocal space) rg_reciprocal63.49 Å
I(0) (reciprocal space) i0_reciprocal661100000.0000
Solution quality estimate total_estimate0.7593
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary46.0 Å
Skewness Skewness skewness0.633
Kurtosis Kurtosis kurtosis-0.326
Angular range angular_range— – 0.1200 Å−1
Current regularization parameter α current_alpha0.0008
Highest regularization parameter α highest_alpha23970000.0000
Real-space data points n_real_points25
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.594; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.582; Smooth: 0.506
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)