6HON

Drosophila NOT4 CBM peptide bound to human CAF40


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A conserved CAF40-binding motif in metazoan NOT4 mediates association with the CCR4-NOT complex.

Keskeny, C.Raisch, T.Sgromo, A.Igreja, C.Bhandari, D.Weichenrieder, O.Izaurralde, E.

(2019) Genes Dev 33: 236-252

  • DOI: 10.1101/gad.320952.118
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The multisubunit CCR4-NOT mRNA deadenylase complex plays important roles in the posttranscriptional regulation of gene expression. The NOT4 E3 ubiquitin ligase is a stable component of the CCR4-NOT complex in yeast but does not copurify with the huma ...

    The multisubunit CCR4-NOT mRNA deadenylase complex plays important roles in the posttranscriptional regulation of gene expression. The NOT4 E3 ubiquitin ligase is a stable component of the CCR4-NOT complex in yeast but does not copurify with the human or Drosophila melanogaster complex. Here we show that the C-terminal regions of human and D. melanogaster NOT4 contain a conserved sequence motif that directly binds the CAF40 subunit of the CCR4-NOT complex (CAF40-binding motif [CBM]). In addition, nonconserved sequences flanking the CBM also contact other subunits of the complex. Crystal structures of the CBM-CAF40 complex reveal a mutually exclusive binding surface for NOT4 and Roquin or Bag of marbles mRNA regulatory proteins. Furthermore, CAF40 depletion or structure-guided mutagenesis to disrupt the NOT4-CAF40 interaction impairs the ability of NOT4 to elicit decay of tethered reporter mRNAs in cells. Together with additional sequence analyses, our results reveal the molecular basis for the association of metazoan NOT4 with the CCR4-NOT complex and show that it deviates substantially from yeast. They mark the NOT4 ubiquitin ligase as an ancient but nonconstitutive cofactor of the CCR4-NOT deadenylase with potential recruitment and/or effector functions.


    Organizational Affiliation

    Department of Biochemistry, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CCR4-NOT transcription complex subunit 9
A, C
273Homo sapiensMutation(s): 0 
Gene Names: CNOT9RCD1RQCD1
Find proteins for Q92600 (Homo sapiens)
Go to UniProtKB:  Q92600
NIH Common Fund Data Resources
PHAROS  Q92600
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CCR4-NOT transcription complex subunit 4, isoform L
B, D
26Drosophila melanogasterMutation(s): 0 
Gene Names: 
Find proteins for M9PCL9 (Drosophila melanogaster)
Go to UniProtKB:  M9PCL9
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.63α = 90
b = 90.32β = 90
c = 196.99γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-02-06
    Type: Initial release
  • Version 1.1: 2019-02-13
    Changes: Data collection, Database references