3UC9

Crystal Structure of Yeast Irc6p - A Novel Type of Conserved Clathrin Accessory Protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Yeast Irc6p is a novel type of conserved clathrin coat accessory factor related to small G proteins.

Gorynia, S.Lorenz, T.C.Costaguta, G.Daboussi, L.Cascio, D.Payne, G.S.

(2012) Mol Biol Cell 23: 4416-4429

  • DOI: https://doi.org/10.1091/mbc.E12-07-0507
  • Primary Citation of Related Structures:  
    3UC9

  • PubMed Abstract: 

    Clathrin coat accessory proteins play key roles in transport mediated by clathrin-coated vesicles. Yeast Irc6p and the related mammalian p34 are putative clathrin accessory proteins that interact with clathrin adaptor complexes. We present evidence that Irc6p functions in clathrin-mediated traffic between the trans-Golgi network and endosomes, linking clathrin adaptor complex AP-1 and the Rab GTPase Ypt31p. The crystal structure of the Irc6p N-terminal domain revealed a G-protein fold most related to small G proteins of the Rab and Arf families. However, Irc6p lacks G-protein signature motifs and high-affinity GTP binding. Also, mutant Irc6p lacking candidate GTP-binding residues retained function. Mammalian p34 rescued growth defects in irc6 cells, indicating functional conservation, and modeling predicted a similar N-terminal fold in p34. Irc6p and p34 also contain functionally conserved C-terminal regions. Irc6p/p34-related proteins with the same two-part architecture are encoded in genomes of species as diverse as plants and humans. Together these results define Irc6p/p34 as a novel type of conserved clathrin accessory protein and founding members of a new G protein-like family.


  • Organizational Affiliation

    Department of Biological Chemistry, School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Increased recombination centers protein 6233Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: IRC6YFR043C
UniProt
Find proteins for P43615 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P43615 
Go to UniProtKB:  P43615
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43615
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.638α = 90
b = 61.638β = 90
c = 95.144γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
DENZOdata reduction
SHELXDphasing
SHELXEmodel building

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-12
    Type: Initial release
  • Version 1.1: 2012-10-03
    Changes: Database references
  • Version 1.2: 2012-11-28
    Changes: Database references
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references