4CRV

Complex of human CNOT9 and CNOT1 including two tryptophans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A Ddx6-Cnot1 Complex and W-Binding Pockets in Cnot9 Reveal Direct Links between Mirna Target Recognition and Silencing

Chen, Y.Boland, A.Kuzuoglu-Ozturk, D.Bawankar, P.Loh, B.Chang, C.T.Weichenrieder, O.Izaurralde, E.

(2014) Mol.Cell 54: 737

  • DOI: 10.1016/j.molcel.2014.03.034
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • CCR4-NOT is a major effector complex in miRNA-mediated gene silencing. It is recruited to miRNA targets through interactions with tryptophan (W)-containing motifs in TNRC6/GW182 proteins and is required for both translational repression and degradati ...

    CCR4-NOT is a major effector complex in miRNA-mediated gene silencing. It is recruited to miRNA targets through interactions with tryptophan (W)-containing motifs in TNRC6/GW182 proteins and is required for both translational repression and degradation of miRNA targets. Here, we elucidate the structural basis for the repressive activity of CCR4-NOT and its interaction with TNRC6/GW182s. We show that the conserved CNOT9 subunit attaches to a domain of unknown function (DUF3819) in the CNOT1 scaffold. The resulting complex provides binding sites for TNRC6/GW182, and its crystal structure reveals tandem W-binding pockets located in CNOT9. We further show that the CNOT1 MIF4G domain interacts with the C-terminal RecA domain of DDX6, a translational repressor and decapping activator. The crystal structure of this complex demonstrates striking similarity to the eIF4G-eIF4A complex. Together, our data provide the missing physical links in a molecular pathway that connects miRNA target recognition with translational repression, deadenylation, and decapping.


    Organizational Affiliation

    Department of Biochemistry, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1
A
258Homo sapiensMutation(s): 0 
Gene Names: CNOT1 (CDC39, KIAA1007, NOT1)
Find proteins for A5YKK6 (Homo sapiens)
Go to Gene View: CNOT1
Go to UniProtKB:  A5YKK6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CELL DIFFERENTIATION PROTEIN RCD1 HOMOLOG
B
273Homo sapiensMutation(s): 0 
Gene Names: CNOT9 (RCD1, RQCD1)
Find proteins for Q92600 (Homo sapiens)
Go to Gene View: CNOT9
Go to UniProtKB:  Q92600
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
TRP
Query on TRP

Download SDF File 
Download CCD File 
B
TRYPTOPHAN
C11 H12 N2 O2
QIVBCDIJIAJPQS-VIFPVBQESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.176 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 154.070α = 90.00
b = 66.810β = 100.22
c = 71.990γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-07
    Type: Initial release
  • Version 1.1: 2014-06-18
    Type: Database references