7BFP | pdb_00007bfp

Structure of the Integrator cleavage module with INTS4/9/11


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.56 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structure of the catalytic core of the Integrator complex.

Pfleiderer, M.M.Galej, W.P.

(2021) Mol Cell 81: 1246

  • DOI: https://doi.org/10.1016/j.molcel.2021.01.005
  • Primary Citation Related Structures: 
    7BFP, 7BFQ

  • PubMed Abstract: 

    The Integrator is a specialized 3' end-processing complex involved in cleavage and transcription termination of a subset of nascent RNA polymerase II transcripts, including small nuclear RNAs (snRNAs). We provide evidence of the modular nature of the Integrator complex by biochemically characterizing its two subcomplexes, INTS5/8 and INTS10/13/14. Using cryoelectron microscopy (cryo-EM), we determined a 3.5-Å-resolution structure of the INTS4/9/11 ternary complex, which constitutes Integrator's catalytic core. Our structure reveals the spatial organization of the catalytic nuclease INTS11, bound to its catalytically impaired homolog INTS9 via several interdependent interfaces. INTS4, a helical repeat protein, plays a key role in stabilizing nuclease domains and other components. In this assembly, all three proteins form a composite electropositive groove, suggesting a putative RNA binding path within the complex. Comparison with other 3' end-processing machineries points to distinct features and a unique architecture of the Integrator's catalytic module.


  • Organizational Affiliation
    • European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France.

Macromolecule Content 

  • Total Structure Weight: 259.83 kDa 
  • Atom Count: 10,071 
  • Modeled Residue Count: 1,358 
  • Deposited Residue Count: 2,318 
  • Unique protein chains: 4

Macromolecules

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Entity ID: 1
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
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Integrator complex subunit 4B [auth C]979Homo sapiensMutation(s): 0 
Gene Names: INTS4MSTP093
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
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Integrator complex subunit 11C [auth B]645Homo sapiensMutation(s): 0 
Gene Names: INTS11CPSF3LRC68
EC: 3.1.27
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:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
UnknownD [auth U]36Homo sapiensMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.56 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-24
    Type: Initial release
  • Version 1.1: 2021-03-31
    Changes: Database references
  • Version 1.2: 2024-07-10
    Changes: Data collection, Database references, Refinement description