5ONB

Drosophila Bag-of-marbles CBM peptide bound to human CAF40


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

DrosophilaBag-of-marbles directly interacts with the CAF40 subunit of the CCR4-NOT complex to elicit repression of mRNA targets.

Sgromo, A.Raisch, T.Backhaus, C.Keskeny, C.Alva, V.Weichenrieder, O.Izaurralde, E.

(2018) RNA 24: 381-395

  • DOI: 10.1261/rna.064584.117
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • <i>Drosophila melanogaster </i> Bag-of-marbles (Bam) promotes germline stem cell (GSC) differentiation by repressing the expression of mRNAs encoding stem cell maintenance factors. Bam interacts with Benign gonial cell neoplasm (Bgcn) and the CCR4 d ...

    Drosophila melanogaster Bag-of-marbles (Bam) promotes germline stem cell (GSC) differentiation by repressing the expression of mRNAs encoding stem cell maintenance factors. Bam interacts with Benign gonial cell neoplasm (Bgcn) and the CCR4 deadenylase, a catalytic subunit of the CCR4-NOT complex. Bam has been proposed to bind CCR4 and displace it from the CCR4-NOT complex. Here, we investigated the interaction of Bam with the CCR4-NOT complex by using purified recombinant proteins. Unexpectedly, we found that Bam does not interact with CCR4 directly but instead binds to the CAF40 subunit of the complex in a manner mediated by a conserved N-terminal CAF40-binding motif (CBM). The crystal structure of the Bam CBM bound to CAF40 reveals that the CBM peptide adopts an α-helical conformation after binding to the concave surface of the crescent-shaped CAF40 protein. We further show that Bam-mediated mRNA decay and translational repression depend entirely on Bam's interaction with CAF40. Thus, Bam regulates the expression of its mRNA targets by recruiting the CCR4-NOT complex through interaction with CAF40.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CCR4-NOT transcription complex subunit 9
A, C, E, G
273Homo sapiensMutation(s): 0 
Gene Names: CNOT9 (RCD1, RQCD1)
Find proteins for Q92600 (Homo sapiens)
Go to Gene View: CNOT9
Go to UniProtKB:  Q92600
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein bag-of-marbles
B, D, F, H
24Drosophila melanogasterMutation(s): 0 
Gene Names: bam
Find proteins for P22745 (Drosophila melanogaster)
Go to UniProtKB:  P22745
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
G
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.216 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 105.570α = 90.00
b = 200.930β = 90.00
c = 59.600γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-12-27
    Type: Initial release
  • Version 1.1: 2018-03-28
    Type: Data collection, Database references