3R42 | pdb_00003r42

Crystal structure of the yeast vps23 UEV domain in complex with a vps27 PSDP peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 
    0.203 (Depositor), 0.233 (DCC) 
  • R-Value Work: 
    0.182 (Depositor) 
  • R-Value Observed: 
    0.183 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3R42

This is version 1.2 of the entry. See complete history

Literature

Structural basis for endosomal recruitment of ESCRT-I by ESCRT-0 in yeast.

Ren, X.Hurley, J.H.

(2011) EMBO J 30: 2130-2139

  • DOI: https://doi.org/10.1038/emboj.2011.122
  • Primary Citation Related Structures: 
    3R3Q, 3R42

  • PubMed Abstract: 

    The ESCRT-0 and ESCRT-I complexes coordinate the clustering of ubiquitinated cargo with intralumenal budding of the endosomal membrane, two essential steps in vacuolar/lysosomal protein sorting from yeast to humans. The 1.85-Å crystal structure of interacting regions of the yeast ESCRT-0 and ESCRT-I complexes reveals that PSDP motifs of the Vps27 ESCRT-0 subunit bind to a novel electropositive N-terminal site on the UEV domain of the ESCRT-I subunit Vps23 centred on Trp16. This novel site is completely different from the C-terminal part of the human UEV domain that binds to P(S/T)AP motifs of human ESCRT-0 and HIV-1 Gag. Disruption of the novel PSDP-binding site eliminates the interaction in vitro and blocks enrichment of Vps23 in endosome-related class E compartments in yeast cells. However, this site is non-essential for sorting of the ESCRT cargo Cps1. Taken together, these results show how a conserved motif/domain pair can evolve to use strikingly different binding modes in different organisms.


  • Organizational Affiliation
    • Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.

Macromolecule Content 

  • Total Structure Weight: 19.09 kDa 
  • Atom Count: 1,446 
  • Modeled Residue Count: 164 
  • Deposited Residue Count: 171 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease162Saccharomyces cerevisiaeMutation(s): 1 
Gene Names: STP22VPS23YCL008CYCL8C
UniProt
Find proteins for P25604 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P25604 
Go to UniProtKB:  P25604
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25604
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 279Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P40343 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40343 
Go to UniProtKB:  P40343
Entity Groups
UniProt GroupP40343
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free:  0.203 (Depositor), 0.233 (DCC) 
  • R-Value Work:  0.182 (Depositor) 
  • R-Value Observed: 0.183 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.2α = 90
b = 142.381β = 90
c = 32.065γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
autoBUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-05-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Refinement description