4JIO

Bro1 V domain and ubiquitin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.421 
  • R-Value Work: 0.366 
  • R-Value Observed: 0.372 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 10.1016/j.devcel.2013.04.007
  • Primary Citation of 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 ...

    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.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BRO1A, B344Naumovozyma castellii CBS 4309Mutation(s): 3 
Gene Names: BRO1(AMINO ACIDS 370-708), NCAS0B02080, NCAS_0B02080
UniProt
Find proteins for G0VBG6 (Naumovozyma castellii (strain ATCC 76901 / BCRC 22586 / CBS 4309 / NBRC 1992 / NRRL Y-12630))
Explore G0VBG6 
Go to UniProtKB:  G0VBG6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0VBG6
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinC [auth U]76Homo sapiensMutation(s): 1 
Gene Names: UBA52, UBCEP2
UniProt & NIH Common Fund Data Resources
Find proteins for P62987 (Homo sapiens)
Explore P62987 
Go to UniProtKB:  P62987
PHAROS:  P62987
GTEx:  ENSG00000221983 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62987
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		A, B L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.421 
  • R-Value Work: 0.366 
  • R-Value Observed: 0.372 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.43α = 90
b = 92.32β = 90
c = 229.45γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHENIXmodel building
PHENIXrefinement
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing

Structure Validation

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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