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9eoc

Structure of the Integrator arm module containing INTS10/13/14 subunits

Method: ELECTRON MICROSCOPY Dmax: 203.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Integrator complex subunit 13

Homo sapiens

UniProt Q9NVM9

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 1–706 Not recorded Integrator complex subunit 14 × 1 （Q96SY0） Integrator complex subunit 10 × 1 （Q9NVR2） MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.30 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 9EOC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6SN1 Crystal structure of the human INTS13-INTS14 complex Deposited 2019-08-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–706（706 aa）
Not recorded SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；0.1 M Bis-Tris (pH 6.0), 0.75 M AmSO4 and 1% (w/v) PEG 3350
Resolution 2.54 Å R-free 0.244
8PK5 INTS13-INTS14 complex with ZNF609 Deposited 2023-06-25 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–706（706 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Hepes-NaOH pH 6.5 0.9 M Na-Malonate 0.25 % (v/v) Jeffamine ED-2003
Resolution 2.50 Å R-free 0.214
8PK6 INTS13 complex with ZNF655 Deposited 2023-06-25 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 × 2 PDB declaration: dimeric
Chain A 1–27（27 aa）
Chain A 48–256（209 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；100 mM MES pH 6.0, 100 mM MgCl2 and 8% (w/v) polyethylene glycol 6,000
Resolution 3.21 Å R-free 0.333
8PK6 INTS13 complex with ZNF655 Deposited 2023-06-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–27（27 aa）
Chain C 48–256（209 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；100 mM MES pH 6.0, 100 mM MgCl2 and 8% (w/v) polyethylene glycol 6,000
Resolution 3.21 Å R-free 0.333
8PK6 INTS13 complex with ZNF655 Deposited 2023-06-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1–27（27 aa）
Chain E 48–256（209 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；100 mM MES pH 6.0, 100 mM MgCl2 and 8% (w/v) polyethylene glycol 6,000
Resolution 3.21 Å R-free 0.333
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 m 1–706（706 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 m 1–706（706 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 m 1–706（706 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
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 ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–564（564 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 ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–706（706 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 ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–706（706 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

9 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name INT13_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–706； UniProt 1–706

Integrator complex subunit 14

Homo sapiens

UniProt Q96SY0

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 1–518 Not recorded Integrator complex subunit 13 × 1 （Q9NVM9） Integrator complex subunit 10 × 1 （Q9NVR2） MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.30 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 9EOC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6SN1 Crystal structure of the human INTS13-INTS14 complex Deposited 2019-08-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–518（518 aa）
Not recorded SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；0.1 M Bis-Tris (pH 6.0), 0.75 M AmSO4 and 1% (w/v) PEG 3350
Resolution 2.54 Å R-free 0.244
8PK5 INTS13-INTS14 complex with ZNF609 Deposited 2023-06-25 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–518（518 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Hepes-NaOH pH 6.5 0.9 M Na-Malonate 0.25 % (v/v) Jeffamine ED-2003
Resolution 2.50 Å R-free 0.214
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 n 1–518（518 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 n 1–518（518 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 n 1–518（518 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
9EP1 Structure of the Integrator arm module containing INTS10/13/14/15 subunits (state 2) Deposited 2024-03-16 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–518（518 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 ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–518（518 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 ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–518（518 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

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name INT14_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–518； UniProt 1–518

Integrator complex subunit 10

Homo sapiens

UniProt Q9NVR2

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 1–710 Not recorded Integrator complex subunit 13 × 1 （Q9NVM9） Integrator complex subunit 14 × 1 （Q96SY0） MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.30 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 9EOC 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 j 1–710（710 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 j 1–710（710 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 j 1–710（710 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 ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–710（710 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 oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–710（710 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 ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–710（710 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 ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–710（710 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 INT10_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain D； PDBConstruct 1–710； UniProt 1–710

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 9eoc

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9eoc
Deposition date deposition_date2024-03-14
Structure title titleStructure of the Integrator arm module containing INTS10/13/14 subunits
Keywords keywordsIntegrator complex assembly, RNA polymerase II transcription termination, 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_guinier55.09 Å
Radius of gyration Rg (electron density) rg_electron54.83 Å
Forward intensity I(0) i0390428000.00
Molecular weight molecular_weight162680.0 kDa
Excluded volume excluded_volume203080 ų
Envelope volume envelope_volume324690 ų
Hydration-shell volume shell_volume53172 ų
Envelope diameter envelope_diameter220.2 Å
Shell Rg shell_rg51.20 Å
Envelope Rg envelope_rg56.41 Å
Shape Rg shape_rg54.98 Å
Total Rg total_rg54.16 Å
Total atoms total_atoms11437
Residues n_residues1563
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 dmax203.7 Å
Rg (real space) rg_real55.82 Å
Rg uncertainty (real space) rg_real_error3.29 Å
I(0) (real space) i0_real3.9040e+08
I(0) uncertainty (real space) i0_real_error8.2910e+06
Rg (reciprocal space) rg_reciprocal54.48 Å
I(0) (reciprocal space) i0_reciprocal389700000.0000
Solution quality estimate total_estimate0.7628
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary35.1 Å
Skewness Skewness skewness0.591
Kurtosis Kurtosis kurtosis-0.247
Angular range angular_range— – 0.1450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha16980000.0000
Real-space data points n_real_points30
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.579; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.573; Smooth: 0.602
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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8. Citations (1)

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9. Files and Curves (10)