4CT4

CNOT1 MIF4G domain - DDX6 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.169 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural and Biochemical Insights to the Role of the Ccr4- not Complex and Ddx6 ATPase in Microrna Repression.

Mathys, H.Basquin, J.Ozgur, S.Czarnocki-Cieciura, M.Bonneau, F.Aartse, A.Dziembowski, A.Nowotny, M.Conti, E.Filipowicz, W.

(2014) Mol Cell 54: 751

  • DOI: https://doi.org/10.1016/j.molcel.2014.03.036
  • Primary Citation of Related Structures:  
    4CT4, 4CT5, 4CT6, 4CT7, 4CV5

  • PubMed Abstract: 

    MicroRNAs (miRNAs) control gene expression by regulating mRNA translation and stability. The CCR4-NOT complex is a key effector of miRNA function acting downstream of GW182/TNRC6 proteins. We show that miRNA-mediated repression requires the central region of CNOT1, the scaffold protein of CCR4-NOT. A CNOT1 domain interacts with CNOT9, which in turn interacts with the silencing domain of TNRC6 in a tryptophan motif-dependent manner. These interactions are direct, as shown by the structure of a CNOT9-CNOT1 complex with bound tryptophan. Another domain of CNOT1 with an MIF4G fold recruits the DEAD-box ATPase DDX6, a known translational inhibitor. Structural and biochemical approaches revealed that CNOT1 modulates the conformation of DDX6 and stimulates ATPase activity. Structure-based mutations showed that the CNOT1 MIF4G-DDX6 interaction is important for miRNA-mediated repression. These findings provide insights into the repressive steps downstream of the GW182/TNRC6 proteins and the role of the CCR4-NOT complex in posttranscriptional regulation in general.


  • Organizational Affiliation

    Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; University of Basel, 4003 Basel, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1
A, C
258Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for A5YKK6 (Homo sapiens)
Explore A5YKK6 
Go to UniProtKB:  A5YKK6
PHAROS:  A5YKK6
GTEx:  ENSG00000125107 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5YKK6
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PROBABLE ATP-DEPENDENT RNA HELICASE DDX6
B, D
378Homo sapiensMutation(s): 0 
EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for P26196 (Homo sapiens)
Explore P26196 
Go to UniProtKB:  P26196
PHAROS:  P26196
GTEx:  ENSG00000110367 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26196
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.169 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.531α = 90
b = 120.014β = 104.01
c = 78.469γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-07
    Type: Initial release
  • Version 1.1: 2014-06-18
    Changes: Database references
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description