4X86

Crystal structure of BAG6-Ubl4a complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 

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This is version 1.4 of the entry. See complete history


Literature

Structure of a BAG6 (Bcl-2-associated Athanogene 6)-Ubl4a (Ubiquitin-like Protein 4a) Complex Reveals a Novel Binding Interface That Functions in Tail-anchored Protein Biogenesis

Kuwabara, N.Minami, R.Yokota, N.Matsumoto, H.Senda, T.Kawahara, H.Kato, R.

(2015) J Biol Chem 290: 9387-9398

  • DOI: https://doi.org/10.1074/jbc.M114.631804
  • Primary Citation of Related Structures:  
    4X86

  • PubMed Abstract: 

    BAG6 is an essential protein that functions in two distinct biological pathways, ubiquitin-mediated protein degradation of defective polypeptides and tail-anchored (TA) transmembrane protein biogenesis in mammals, although its structural and functional properties remain unknown. We solved a crystal structure of the C-terminal heterodimerization domains of BAG6 and Ubl4a and characterized their interaction biochemically. Unexpectedly, the specificity and structure of the C terminus of BAG6, which was previously classified as a BAG domain, were completely distinct from those of the canonical BAG domain. Furthermore, the tight association of BAG6 and Ubl4a resulted in modulation of Ubl4a protein stability in cells. Therefore, we propose to designate the Ubl4a-binding region of BAG6 as the novel BAG-similar (BAGS) domain. The structure of Ubl4a, which interacts with BAG6, is similar to the yeast homologue Get5, which forms a homodimer. These observations indicate that the BAGS domain of BAG6 promotes the TA protein biogenesis pathway in mammals by the interaction with Ubl4a.


  • Organizational Affiliation

    From the Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan and.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-like protein 4A58Homo sapiensMutation(s): 0 
Gene Names: UBL4A
UniProt & NIH Common Fund Data Resources
Find proteins for P11441 (Homo sapiens)
Explore P11441 
Go to UniProtKB:  P11441
GTEx:  ENSG00000102178 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11441
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Large proline-rich protein BAG681Homo sapiensMutation(s): 0 
Gene Names: BAG6
UniProt & NIH Common Fund Data Resources
Find proteins for P46379 (Homo sapiens)
Explore P46379 
Go to UniProtKB:  P46379
GTEx:  ENSG00000204463 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46379
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.987α = 90
b = 72.987β = 90
c = 48.481γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata reduction
PDB_EXTRACTdata extraction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-25
    Type: Initial release
  • Version 1.1: 2015-03-11
    Changes: Database references
  • Version 1.2: 2015-04-22
    Changes: Database references
  • Version 1.3: 2017-10-04
    Changes: Data collection, Database references, Derived calculations, Source and taxonomy
  • Version 1.4: 2019-10-23
    Changes: Data collection