5AIE | pdb_00005aie

Not4 ring domain in complex with Ubc4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.271 (Depositor), 0.279 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 
    0.225 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5AIE

This is version 1.3 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: https://doi.org/10.1016/j.str.2015.03.011
  • Primary Citation Related Structures: 
    5AIE, 5AJD

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 24.28 kDa 
  • Atom Count: 1,575 
  • Modeled Residue Count: 204 
  • Deposited Residue Count: 215 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 457Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.3.2.27
UniProt
Find proteins for P34909 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P34909 
Go to UniProtKB:  P34909
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34909
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
UBIQUITIN-CONJUGATING ENZYME E2 4158Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt)
UniProt
Find proteins for P15731 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P15731 
Go to UniProtKB:  P15731
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15731
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.271 (Depositor), 0.279 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 0.225 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.112α = 90
b = 107.112β = 90
c = 62.203γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-29
    Type: Initial release
  • Version 1.1: 2015-05-13
    Changes: Database references
  • Version 1.2: 2015-05-27
    Changes: Database references
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other