6UXQ

Crystal structure of BAK core domain BH3-groove-dimer in complex with POPC and C8E4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

BAK core dimers bind lipids and can be bridged by them.

Cowan, A.D.Smith, N.A.Sandow, J.J.Kapp, E.A.Rustam, Y.H.Murphy, J.M.Brouwer, J.M.Bernardini, J.P.Roy, M.J.Wardak, A.Z.Tan, I.K.Webb, A.I.Gulbis, J.M.Smith, B.J.Reid, G.E.Dewson, G.Colman, P.M.Czabotar, P.E.

(2020) Nat Struct Mol Biol 27: 1024-1031

  • DOI: 10.1038/s41594-020-0494-5
  • Primary Citation of Related Structures:  
    6UXR, 6UXQ, 6UXN, 6UXM, 6UXP, 6UXO

  • PubMed Abstract: 
  • BAK and BAX are essential mediators of apoptosis that oligomerize in response to death cues, thereby causing permeabilization of the mitochondrial outer membrane. Their transition from quiescent monomers to pore-forming oligomers involves a well-characterized symmetric dimer intermediate ...

    BAK and BAX are essential mediators of apoptosis that oligomerize in response to death cues, thereby causing permeabilization of the mitochondrial outer membrane. Their transition from quiescent monomers to pore-forming oligomers involves a well-characterized symmetric dimer intermediate. However, no essential secondary interface that can be disrupted by mutagenesis has been identified. Here we describe crystal structures of human BAK core domain (α2-α5) dimers that reveal preferred binding sites for membrane lipids and detergents. The phospholipid headgroup and one acyl chain (sn2) associate with one core dimer while the other acyl chain (sn1) associates with a neighboring core dimer, suggesting a mechanism by which lipids contribute to the oligomerization of BAK. Our data support a model in which, unlike for other pore-forming proteins whose monomers assemble into oligomers primarily through protein-protein interfaces, the membrane itself plays a role in BAK and BAX oligomerization.


    Organizational Affiliation

    Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia. czabotar@wehi.edu.au.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bcl-2 homologous antagonist/killerA, B, C, D85Homo sapiensMutation(s): 0 
Gene Names: BAK1BAKBCL2L7CDN1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q16611 (Homo sapiens)
Explore Q16611 
Go to UniProtKB:  Q16611
PHAROS:  Q16611
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LBN
Query on LBN

Download Ideal Coordinates CCD File 
L [auth B]1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
C42 H82 N O8 P
WTJKGGKOPKCXLL-VYOBOKEXSA-N
 Ligand Interaction
C8E
Query on C8E

Download Ideal Coordinates CCD File 
G [auth A], H [auth A], I [auth A], K [auth B], M [auth B], O [auth B], R [auth C], S [auth D](HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
C16 H34 O5
FEOZZFHAVXYAMB-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], N [auth B], T [auth D]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
J [auth A], P [auth B], Q [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.318α = 90
b = 150.086β = 90
c = 51.749γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia1079706
National Health and Medical Research Council (NHMRC, Australia)Australia1059290
National Health and Medical Research Council (NHMRC, Australia)Australia1113133

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-02
    Type: Initial release
  • Version 1.1: 2020-09-30
    Changes: Database references
  • Version 1.2: 2020-11-18
    Changes: Database references