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 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1074/jbc.M114.631804

  • 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 function ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-like protein 4A
A
58Homo sapiensMutation(s): 0 
Gene Names: UBL4A (DXS254E, GDX, UBL4)
Find proteins for P11441 (Homo sapiens)
Go to Gene View: UBL4A
Go to UniProtKB:  P11441
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Large proline-rich protein BAG6
B
81Homo sapiensMutation(s): 0 
Gene Names: BAG6 (BAT3, G3)
Find proteins for P46379 (Homo sapiens)
Go to Gene View: BAG6
Go to UniProtKB:  P46379
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CPS
Query on CPS

Download SDF File 
Download CCD File 
B
3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
CHAPS
C32 H58 N2 O7 S
UMCMPZBLKLEWAF-BCTGSCMUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.204 
  • Space Group: P 62
Unit Cell:
Length (Å)Angle (°)
a = 72.987α = 90.00
b = 72.987β = 90.00
c = 48.481γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
Aimlessdata scaling
PHENIXphasing
Aimlessdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-12-10 
  • Released Date: 2015-02-25 
  • Deposition Author(s): Kuwabara, N., Kato, R.

Revision History 

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