4JJY | pdb_00004jjy

Alix V domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.50 Å
  • R-Value Free: 
    0.283 (Depositor), 0.265 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4JJY

This is version 1.2 of the entry. See complete history

Literature

The yeast alix homolog bro1 functions as a ubiquitin receptor for protein sorting into multivesicular endosomes.

Pashkova, N.Gakhar, L.Winistorfer, S.C.Sunshine, A.B.Rich, M.Dunham, M.J.Yu, L.Piper, R.C.

(2013) Dev Cell 25: 520-533

  • DOI: https://doi.org/10.1016/j.devcel.2013.04.007
  • Primary Citation Related Structures: 
    4JIO, 4JJY

  • PubMed Abstract: 

    Sorting of ubiquitinated membrane proteins into lumenal vesicles of multivesicular bodies is mediated by the Endosomal Sorting Complex Required for Transport (ESCRT) apparatus and accessory proteins such as Bro1, which recruits the deubiquitinating enzyme Doa4 to remove ubiquitin from cargo. Here we propose that Bro1 works as a receptor for the selective sorting of ubiquitinated cargoes. We found synthetic genetic interactions between BRO1 and ESCRT-0, suggesting that Bro1 functions similarly to ESCRT-0. Multiple structural approaches demonstrated that Bro1 binds ubiquitin via the N-terminal trihelical arm of its middle V domain. Mutants of Bro1 that lack the ability to bind Ub were dramatically impaired in their ability to sort Ub-cargo membrane proteins, but only when combined with hypomorphic alleles of ESCRT-0. These data suggest that Bro1 and other Bro1 family members function in parallel with ESCRT-0 to recognize and sort Ub-cargoes.


  • Organizational Affiliation
    • Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA 52242, USA.

Macromolecule Content 

  • Total Structure Weight: 81.8 kDa 
  • Atom Count: 5,396 
  • Modeled Residue Count: 684 
  • Deposited Residue Count: 720 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Programmed cell death 6-interacting protein
A, B
360Homo sapiensMutation(s): 0 
Gene Names: PDCD6IPAIP1ALIXKIAA1375
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WUM4 (Homo sapiens)
Explore Q8WUM4 
Go to UniProtKB:  Q8WUM4
PHAROS:  Q8WUM4
GTEx:  ENSG00000170248 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WUM4
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.50 Å
  • R-Value Free:  0.283 (Depositor), 0.265 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 223.77α = 90
b = 223.77β = 90
c = 223.77γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHENIXmodel building
PHENIXrefinement
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-19
    Type: Initial release
  • Version 1.1: 2013-07-10
    Changes: Database references
  • Version 1.2: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary