8UIB

Structure of the human INTS9-INTS11-BRAT1 complex

  • Classification: RNA BINDING PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Trichoplusia ni
  • Mutation(s): No 

  • Deposited: 2023-10-10 Released: 2024-08-21 
  • Deposition Author(s): Lin, M., Tong, L.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Cancer Prevention and Research Institute of Texas (CPRIT)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.21 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Cytoplasmic binding partners of the Integrator endonuclease INTS11 and its paralog CPSF73 are required for their nuclear function.

Lin, M.H.Jensen, M.K.Elrod, N.D.Chu, H.F.Haseley, M.Beam, A.C.Huang, K.L.Chiang, W.Russell, W.K.Williams, K.Proschel, C.Wagner, E.J.Tong, L.

(2024) Mol Cell 84: 2900-2917.e10

  • DOI: https://doi.org/10.1016/j.molcel.2024.06.017
  • Primary Citation of Related Structures:  
    8UIB, 8UIC

  • PubMed Abstract: 

    INTS11 and CPSF73 are metal-dependent endonucleases for Integrator and pre-mRNA 3'-end processing, respectively. Here, we show that the INTS11 binding partner BRAT1/CG7044, a factor important for neuronal fitness, stabilizes INTS11 in the cytoplasm and is required for Integrator function in the nucleus. Loss of BRAT1 in neural organoids leads to transcriptomic disruption and precocious expression of neurogenesis-driving transcription factors. The structures of the human INTS9-INTS11-BRAT1 and Drosophila dIntS11-CG7044 complexes reveal that the conserved C terminus of BRAT1/CG7044 is captured in the active site of INTS11, with a cysteine residue directly coordinating the metal ions. Inspired by these observations, we find that UBE3D is a binding partner for CPSF73, and UBE3D likely also uses a conserved cysteine residue to directly coordinate the active site metal ions. Our studies have revealed binding partners for INTS11 and CPSF73 that behave like cytoplasmic chaperones with a conserved impact on the nuclear functions of these enzymes.


  • Organizational Affiliation

    Department of Biological Sciences, Columbia University, New York, NY 10027, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 9A [auth I]658Homo sapiensMutation(s): 0 
Gene Names: INTS9
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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 11B [auth K]600Homo 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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
BRCA1-associated ATM activator 1C [auth T]821Homo 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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.21 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM134539
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM118093
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesRP170593

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-21
    Type: Initial release