8R2D

Integrator cleavage module assembly intermediate

  • Classification: TRANSCRIPTION
  • Organism(s): Homo sapiens
  • Expression System: Trichoplusia ni
  • Mutation(s): No 

  • Deposited: 2023-11-03 Released: 2024-07-31 
  • Deposition Author(s): Sabath, K., Qiu, C., Jonas, S.
  • Funding Organization(s): Swiss National Science Foundation, Swiss State Secretariat for Education, Research and Innovation, European Molecular Biology Organization (EMBO), ETH Zurich, German Academic Scholarship Foundation

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Assembly mechanism of Integrator's RNA cleavage module.

Sabath, K.Qiu, C.Jonas, S.

(2024) Mol Cell 84: 2882-2899.e10

  • DOI: https://doi.org/10.1016/j.molcel.2024.06.032
  • Primary Citation of Related Structures:  
    8R22, 8R23, 8R2D

  • PubMed Abstract: 

    The modular Integrator complex is a transcription regulator that is essential for embryonic development. It attenuates coding gene expression via premature transcription termination and performs 3'-processing of non-coding RNAs. For both activities, Integrator requires endonuclease activity that is harbored by an RNA cleavage module consisting of INTS4-9-11. How correct assembly of Integrator modules is achieved remains unknown. Here, we show that BRAT1 and WDR73 are critical biogenesis factors for the human cleavage module. They maintain INTS9-11 inactive during maturation by physically blocking the endonuclease active site and prevent premature INTS4 association. Furthermore, BRAT1 facilitates import of INTS9-11 into the nucleus, where it is joined by INTS4. Final BRAT1 release requires locking of the mature cleavage module conformation by inositol hexaphosphate (IP 6 ). Our data explain several neurodevelopmental disorders caused by BRAT1, WDR73, and INTS11 mutations as Integrator assembly defects and reveal that IP 6 is an essential co-factor for cleavage module maturation.


  • Organizational Affiliation

    Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BRCA1-associated ATM activator 1827Homo sapiensMutation(s): 0 
Gene Names: BRAT1
UniProt & NIH Common Fund Data Resources
Find proteins for Q6PJG6 (Homo sapiens)
Explore Q6PJG6 
Go to UniProtKB:  Q6PJG6
PHAROS:  Q6PJG6
GTEx:  ENSG00000106009 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6PJG6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 9658Homo sapiensMutation(s): 0 
Gene Names: INTS9RC74
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NV88 (Homo sapiens)
Explore Q9NV88 
Go to UniProtKB:  Q9NV88
PHAROS:  Q9NV88
GTEx:  ENSG00000104299 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NV88
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 11612Homo sapiensMutation(s): 0 
Gene Names: INTS11
UniProt & NIH Common Fund Data Resources
Find proteins for Q5TA45 (Homo sapiens)
Explore Q5TA45 
Go to UniProtKB:  Q5TA45
PHAROS:  Q5TA45
GTEx:  ENSG00000127054 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5TA45
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 4973Homo sapiensMutation(s): 0 
Gene Names: INTS4
UniProt & NIH Common Fund Data Resources
Find proteins for Q96HW7 (Homo sapiens)
Explore Q96HW7 
Go to UniProtKB:  Q96HW7
PHAROS:  Q96HW7
GTEx:  ENSG00000149262 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96HW7
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland141735
Swiss National Science FoundationSwitzerland182880
Swiss National Science FoundationSwitzerland205601
Swiss National Science FoundationSwitzerland31003A_179498
Swiss State Secretariat for Education, Research and InnovationSwitzerlandMB22.00064
European Molecular Biology Organization (EMBO)European Union4918
ETH ZurichSwitzerlandETH-31 18-1
German Academic Scholarship FoundationGermanyKevin Sabath

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-31
    Type: Initial release
  • Version 1.1: 2024-08-21
    Changes: Data collection, Database references