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- PDB-9ep1: Structure of the Integrator arm module containing INTS10/13/14/15... -

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Basic information

Entry
Database: PDB / ID: 9ep1
TitleStructure of the Integrator arm module containing INTS10/13/14/15 subunits (state 2)
Components
  • Integrator complex subunit 10
  • Integrator complex subunit 13
  • Integrator complex subunit 14
  • Integrator complex subunit 15
KeywordsTRANSCRIPTION / Integrator complex assembly / RNA polymerase II transcription termination / transcription factors
Function / homology
Function and homology information


regulation of fertilization / snRNA 3'-end processing / snRNA processing / INTAC complex / protein localization to nuclear envelope / eye development / regulation of transcription elongation by RNA polymerase II / flagellated sperm motility / integrator complex / RNA polymerase II transcription initiation surveillance ...regulation of fertilization / snRNA 3'-end processing / snRNA processing / INTAC complex / protein localization to nuclear envelope / eye development / regulation of transcription elongation by RNA polymerase II / flagellated sperm motility / integrator complex / RNA polymerase II transcription initiation surveillance / centrosome localization / RNA polymerase II transcribes snRNA genes / regulation of mitotic cell cycle / mitotic spindle organization / mRNA splicing, via spliceosome / brain development / chromosome / DNA-binding transcription factor binding / nuclear body / cell division / intracellular membrane-bounded organelle / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Integrator complex subunit 10 / Integrator complex subunit 15 / Integrator complex subunit 14 / Integrator complex subunit 14, beta-barrel domain / Integrator complex subunit 14, C-terminal / Integrator complex subunit 15 / Integrator complex subunit 14, beta-barrel domain / Integrator complex subunit 14, alpha-helical domain / Integrator subunit 10 / Cell cycle regulator Mat89Bb ...Integrator complex subunit 10 / Integrator complex subunit 15 / Integrator complex subunit 14 / Integrator complex subunit 14, beta-barrel domain / Integrator complex subunit 14, C-terminal / Integrator complex subunit 15 / Integrator complex subunit 14, beta-barrel domain / Integrator complex subunit 14, alpha-helical domain / Integrator subunit 10 / Cell cycle regulator Mat89Bb / Cell cycle and development regulator Mat89Bb / von Willebrand factor type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
Integrator complex subunit 15 / Integrator complex subunit 14 / Integrator complex subunit 13 / Integrator complex subunit 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsRazew, M. / Galej, W.P.
Funding support Germany, 1items
OrganizationGrant numberCountry
EIPOD fellowship under Marie Sklodowska-Curie Actions COFUND Germany
CitationJournal: Mol Cell / Year: 2024
Title: Structural basis of the Integrator complex assembly and association with transcription factors.
Authors: Michal Razew / Angelique Fraudeau / Moritz M Pfleiderer / Romain Linares / Wojciech P Galej /
Abstract: Integrator is a multi-subunit protein complex responsible for premature transcription termination of coding and non-coding RNAs. This is achieved via two enzymatic activities, RNA endonuclease and ...Integrator is a multi-subunit protein complex responsible for premature transcription termination of coding and non-coding RNAs. This is achieved via two enzymatic activities, RNA endonuclease and protein phosphatase, acting on the promoter-proximally paused RNA polymerase Ⅱ (RNAPⅡ). Yet, it remains unclear how Integrator assembly and recruitment are regulated and what the functions of many of its core subunits are. Here, we report the structures of two human Integrator sub-complexes: INTS10/13/14/15 and INTS5/8/10/15, and an integrative model of the fully assembled Integrator bound to the RNAPⅡ paused elongating complex (PEC). An in silico protein-protein interaction screen of over 1,500 human transcription factors (TFs) identified ZNF655 as a direct interacting partner of INTS13 within the fully assembled Integrator. We propose a model wherein INTS13 acts as a platform for the recruitment of TFs that could modulate the stability of the Integrator's association at specific loci and regulate transcription attenuation of the target genes.
History
DepositionMar 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release
Revision 1.0Jun 12, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.1Jul 24, 2024Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first / _em_admin.last_update
Revision 1.2Jul 9, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 9, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrator complex subunit 13
B: Integrator complex subunit 14
C: Integrator complex subunit 15
D: Integrator complex subunit 10


Theoretical massNumber of molelcules
Total (without water)247,6934
Polymers247,6934
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Integrator complex subunit 13 / Cell cycle regulator Mat89Bb homolog / Germ cell tumor 1 / Protein asunder homolog / Sarcoma antigen NY-SAR-95


Mass: 63873.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS13, ASUN, C12orf11, GCT1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NVM9
#2: Protein Integrator complex subunit 14 / von Willebrand factor A domain-containing protein 9


Mass: 57526.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS14, C15orf44, VWA9 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96SY0
#3: Protein Integrator complex subunit 15


Mass: 43952.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS15, C7orf26 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96N11
#4: Protein Integrator complex subunit 10 / Int10


Mass: 82339.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS10, C8orf35 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NVR2
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Structure of the Integrator arm module containing INTS10/13/14/15 subunits (state 2)
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.27 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: LAB6 / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 54007 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00314612
ELECTRON MICROSCOPYf_angle_d0.59219901
ELECTRON MICROSCOPYf_dihedral_angle_d4.92030
ELECTRON MICROSCOPYf_chiral_restr0.0392379
ELECTRON MICROSCOPYf_plane_restr0.0042554

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