5FU7

drosophila nanos NBR peptide bound to the NOT module of the human CCR4-NOT complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Distinct Modes of Recruitment of the Ccr4-not Complex by Drosophila and Vertebrate Nanos

Raisch, T.Bhandari, D.Sabath, K.Helms, S.Valkov, E.Weichenrieder, O.Izaurralde, E.

(2016) EMBO J 35: 974

  • DOI: https://doi.org/10.15252/embj.201593634
  • Primary Citation of Related Structures:  
    5FU6, 5FU7

  • PubMed Abstract: 

    Nanos proteins repress the expression of target mRNAs by recruiting effector complexes through non-conserved N-terminal regions. In vertebrates, Nanos proteins interact with the NOT1 subunit of the CCR4-NOT effector complex through a NOT1 interacting motif (NIM), which is absent in Nanos orthologs from several invertebrate species. Therefore, it has remained unclear whether the Nanos repressive mechanism is conserved and whether it also involves direct interactions with the CCR4-NOT deadenylase complex in invertebrates. Here, we identify an effector domain (NED) that is necessary for the Drosophila melanogaster (Dm) Nanos to repress mRNA targets. The NED recruits the CCR4-NOT complex through multiple and redundant binding sites, including a central region that interacts with the NOT module, which comprises the C-terminal domains of NOT1-3. The crystal structure of the NED central region bound to the NOT module reveals an unanticipated bipartite binding interface that contacts NOT1 and NOT3 and is distinct from the NIM of vertebrate Nanos. Thus, despite the absence of sequence conservation, the N-terminal regions of Nanos proteins recruit CCR4-NOT to assemble analogous repressive complexes.


  • Organizational Affiliation

    Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1
A, E
535Homo sapiensMutation(s): 3 
UniProt & NIH Common Fund Data Resources
Find proteins for A5YKK6 (Homo sapiens)
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Go to UniProtKB:  A5YKK6
PHAROS:  A5YKK6
GTEx:  ENSG00000125107 
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UniProt GroupA5YKK6
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 2
B, F
197Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZN8 (Homo sapiens)
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Go to UniProtKB:  Q9NZN8
PHAROS:  Q9NZN8
GTEx:  ENSG00000111596 
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UniProt GroupQ9NZN8
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3
C, G
148Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O75175 (Homo sapiens)
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PHAROS:  O75175
GTEx:  ENSG00000088038 
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UniProt GroupO75175
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NANOS, ISOFORM B
D, H
54Drosophila melanogasterMutation(s): 0 
UniProt
Find proteins for A0A0B4KGY5 (Drosophila melanogaster)
Explore A0A0B4KGY5 
Go to UniProtKB:  A0A0B4KGY5
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UniProt GroupA0A0B4KGY5
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.95α = 90
b = 135.67β = 107.98
c = 104.97γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-23
    Type: Initial release
  • Version 1.1: 2016-05-18
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Other, Refinement description