4J8S | pdb_00004j8s

Crystal structure of human CNOT1 MIF4G domain in complex with a TTP peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 
    0.188 (Depositor), 0.184 (DCC) 
  • R-Value Work: 
    0.167 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 
    0.168 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4J8S

This is version 1.3 of the entry. See complete history

Literature

Structural basis for the recruitment of the human CCR4-NOT deadenylase complex by tristetraprolin.

Fabian, M.R.Frank, F.Rouya, C.Siddiqui, N.Lai, W.S.Karetnikov, A.Blackshear, P.J.Nagar, B.Sonenberg, N.

(2013) Nat Struct Mol Biol 20: 735-739

  • DOI: https://doi.org/10.1038/nsmb.2572
  • Primary Citation Related Structures: 
    4J8S

  • PubMed Abstract: 

    Tristetraprolin (TTP) is an RNA-binding protein that controls the inflammatory response by limiting the expression of several proinflammatory cytokines. TTP post-transcriptionally represses gene expression by interacting with AU-rich elements (AREs) in 3' untranslated regions of target mRNAs and subsequently engenders their deadenylation and decay. TTP accomplishes these tasks, at least in part, by recruiting the multisubunit CCR4-NOT deadenylase complex to the mRNA. Here we identify an evolutionarily conserved C-terminal motif in human TTP that directly binds a central domain of CNOT1, a core subunit of the CCR4-NOT complex. A high-resolution crystal structure of the TTP-CNOT1 complex was determined, providing the first structural insight, to our knowledge, into an ARE-binding protein bound to the CCR4-NOT complex. Mutations at the CNOT1-TTP interface impair TTP-mediated deadenylation, demonstrating the significance of this interaction in TTP-mediated gene silencing.


  • Organizational Affiliation
    • Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada. marc.fabian@mcgill.ca

Macromolecule Content 

  • Total Structure Weight: 25.79 kDa 
  • Atom Count: 1,872 
  • Modeled Residue Count: 192 
  • Deposited Residue Count: 218 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CCR4-NOT transcription complex subunit 1203Homo sapiensMutation(s): 0 
Gene Names: AD-005CDC39CNOT1KIAA1007NOT1
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
Tristetraprolin15Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P26651 (Homo sapiens)
Explore P26651 
Go to UniProtKB:  P26651
PHAROS:  P26651
GTEx:  ENSG00000128016 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26651
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free:  0.188 (Depositor), 0.184 (DCC) 
  • R-Value Work:  0.167 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 0.168 (Depositor) 
Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.06α = 90
b = 85.06β = 90
c = 85.06γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SHELXSphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-08
    Type: Initial release
  • Version 1.1: 2013-07-24
    Changes: Database references
  • Version 1.2: 2016-05-25
    Changes: Structure summary
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references