5ANR

Structure of a human 4E-T - DDX6 - CNOT1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of a Human 4E-T/Ddx6/Cnot1 Complex Reveals the Different Interplay of Ddx6-Binding Proteins with the Ccr4-not Complex.

Ozgur, S.Basquin, J.Kamenska, A.Filipowicz, W.Standart, N.Conti, E.

(2015) Cell Rep 13: 703

  • DOI: https://doi.org/10.1016/j.celrep.2015.09.033
  • Primary Citation of Related Structures:  
    5ANR

  • PubMed Abstract: 

    The DEAD-box protein DDX6 is a central component of translational repression mechanisms in maternal mRNA storage in oocytes and microRNA-mediated silencing in somatic cells. DDX6 interacts with the CCR4-NOT complex and functions in concert with several post-transcriptional regulators, including Edc3, Pat1, and 4E-T. We show that the conserved CUP-homology domain (CHD) of human 4E-T interacts directly with DDX6 in both the presence and absence of the central MIF4G domain of CNOT1. The 2.1-Å resolution structure of the corresponding ternary complex reveals how 4E-T CHD wraps around the RecA2 domain of DDX6 and contacts CNOT1. Although 4E-T CHD lacks recognizable sequence similarity with Edc3 or Pat1, it shares the same DDX6-binding surface. In contrast to 4E-T, however, the Edc3 and Pat1 FDF motifs dissociate from DDX6 upon CNOT1 MIF4G binding in vitro. The results underscore the presence of a complex network of simultaneous and/or mutually exclusive interactions in DDX6-mediated repression.


  • Organizational Affiliation

    Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried/Munich, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1258Homo 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
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PROBABLE ATP-DEPENDENT RNA HELICASE DDX6378Homo 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
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
EUKARYOTIC TRANSLATION INITIATION FACTOR 4E TRANSPORTER44Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NRA8 (Homo sapiens)
Explore Q9NRA8 
Go to UniProtKB:  Q9NRA8
PHAROS:  Q9NRA8
GTEx:  ENSG00000184708 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NRA8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.129α = 90
b = 93.129β = 90
c = 175.329γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-21
    Type: Initial release
  • Version 1.1: 2016-04-27
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Other, Refinement description