3UC9

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1091/mbc.E12-07-0507

  • 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 t ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Increased recombination centers protein 6
A
233Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: IRC6
Find proteins for P43615 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P43615
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.197 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 61.638α = 90.00
b = 61.638β = 90.00
c = 95.144γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
SHELXDphasing
DENZOdata reduction
SHELXEmodel building
PDB_EXTRACTdata extraction
ADSCdata collection
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-09-12
    Type: Initial release
  • Version 1.1: 2012-10-03
    Type: Database references
  • Version 1.2: 2012-11-28
    Type: Database references