5AIE

Not4 ring domain in complex with Ubc4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Architecture of the Ubiquitylation Module of the Yeast Ccr4-not Complex.

Bhaskar, V.Basquin, J.Conti, E.

(2015) Structure 23: 921

  • DOI: 10.1016/j.str.2015.03.011
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Ccr4-Not complex regulates eukaryotic gene expression at multiple levels, including mRNA turnover, translational repression, and transcription. We have studied the ubiquitylation module of the yeast Ccr4-Not complex and addressed how E3 ligase bi ...

    The Ccr4-Not complex regulates eukaryotic gene expression at multiple levels, including mRNA turnover, translational repression, and transcription. We have studied the ubiquitylation module of the yeast Ccr4-Not complex and addressed how E3 ligase binds cognate E2 and how it is tethered to the complex. The 2.8-Å resolution crystal structure of the N-terminal RING domain of Not4 in complex with Ubc4 shows the detailed interactions of this E3-E2 complex. The 3.6-Å resolution crystal structure of the C-terminal domain of the yeast Not4 in complex with the C-terminal domain of Not1 reveals how a largely extended region at the C-terminus of Not4 wraps around a HEAT-repeat region of Not1. This C-terminal region of Not4 is only partly conserved in metazoans, rationalizing its weaker Not1-binding properties. The structural and biochemical data show how Not1 can incorporate both the ubiquitylation module and the Not2-Not3/5 module concomitantly in the Ccr4-Not complex.


    Organizational Affiliation

    Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Munich, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 4
A
57Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MOT2 (CCL1, NOT4, SIG1, SSF1)
Find proteins for P34909 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P34909
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
UBIQUITIN-CONJUGATING ENZYME E2 4
B
158Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: UBC4
EC: 2.3.2.23
Find proteins for P15731 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P15731
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.220 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 107.112α = 90.00
b = 107.112β = 90.00
c = 62.203γ = 120.00
Software Package:
Software NamePurpose
XDSdata scaling
PHENIXrefinement
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-04-29
    Type: Initial release
  • Version 1.1: 2015-05-13
    Type: Database references
  • Version 1.2: 2015-05-27
    Type: Database references