4CQO | pdb_00004cqo

Structure of the human CNOT1 superfamily homology domain in complex with a Nanos1 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.243 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.222 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.223 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4CQO

This is version 1.2 of the entry. See complete history

Literature

Structural Basis for the Nanos-Mediated Recruitment of the Ccr4-not Complex and Translational Repression

Bhandari, D.Raisch, T.Weichenrieder, O.Jonas, S.Izaurralde, E.

(2014) Genes Dev 28: 888

  • DOI: https://doi.org/10.1101/gad.237289.113
  • Primary Citation Related Structures: 
    4CQO

  • PubMed Abstract: 

    The RNA-binding proteins of the Nanos family play an essential role in germ cell development and survival in a wide range of metazoan species. They function by suppressing the expression of target mRNAs through the recruitment of effector complexes, which include the CCR4-NOT deadenylase complex. Here, we show that the three human Nanos paralogs (Nanos1-3) interact with the CNOT1 C-terminal domain and determine the structural basis for the specific molecular recognition. Nanos1-3 bind CNOT1 through a short CNOT1-interacting motif (NIM) that is conserved in all vertebrates and some invertebrate species. The crystal structure of the human Nanos1 NIM peptide bound to CNOT1 reveals that the peptide opens a conserved hydrophobic pocket on the CNOT1 surface by inserting conserved aromatic residues. The substitutions of these aromatic residues in the Nanos1-3 NIMs abolish binding to CNOT1 and abrogate the ability of the proteins to repress translation. Our findings provide the structural basis for the recruitment of the CCR4-NOT complex by vertebrate Nanos, indicate that the NIMs are the major determinants of the translational repression mediated by Nanos, and identify the CCR4-NOT complex as the main effector complex for Nanos function.


  • Organizational Affiliation
    • Department of Biochemistry, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.

Macromolecule Content 

  • Total Structure Weight: 126.89 kDa 
  • Atom Count: 8,624 
  • Modeled Residue Count: 1,055 
  • Deposited Residue Count: 1,104 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1
A, C
535Homo 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:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
NANOS HOMOLOG 1
B, D
17Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WY41 (Homo sapiens)
Explore Q8WY41 
Go to UniProtKB:  Q8WY41
PHAROS:  Q8WY41
GTEx:  ENSG00000188613 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WY41
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.243 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.222 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.223 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.53α = 90
b = 167.33β = 90
c = 112.04γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-23
    Type: Initial release
  • Version 1.1: 2014-04-30
    Changes: Database references
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Other, Refinement description