8SPF

Crystal structure of Bax core domain BH3-groove dimer - hexameric fraction with 2-stearoyl lysoPC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.257 

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Literature

Sequence differences between BAX and BAK core domains manifest as differences in their interactions with lipids.

Miller, M.S.Cowan, A.D.Brouwer, J.M.Smyth, S.T.Peng, L.Wardak, A.Z.Uren, R.T.Luo, C.Roy, M.J.Shah, S.Tan, Z.Reid, G.E.Colman, P.M.Czabotar, P.E.

(2023) FEBS J 

  • DOI: https://doi.org/10.1111/febs.17031
  • Primary Citation of Related Structures:  
    8G1T, 8SPE, 8SPF, 8SPZ, 8SRX, 8SRY, 8SVK

  • PubMed Abstract: 

    The B-cell lymphoma 2 (BCL2) family members, BCL2-associated protein X (BAX) and BCL2 homologous antagonist killer (BAK), are required for programmed cell death via the mitochondrial pathway. When cells are stressed, damaged or redundant, the balance of power between the BCL2 family of proteins shifts towards BAX and BAK, allowing their transition from an inactive, monomeric state to a membrane-active oligomeric form that releases cytochrome c from the mitochondrial intermembrane space. That oligomeric state has an essential intermediate, a symmetric homodimer of BAX or BAK. Here we describe crystal structures of dimers of the core domain of BAX, comprising its helices α2-α5. These structures provide an atomic resolution description of the interactions that drive BAX homo-dimerisation and insights into potential interaction between core domain dimers and membrane lipids. The previously identified BAK lipid-interacting sites are not conserved with BAX and are likely to determine the differences between them in their interactions with lipids. We also describe structures of heterodimers of BAK/BAX core domains, yielding further insight into the differences in lipid binding between BAX and BAK.


  • Organizational Affiliation

    Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Apoptosis regulator BAX81Homo sapiensMutation(s): 0 
Gene Names: BAXBCL2L4
UniProt & NIH Common Fund Data Resources
Find proteins for Q07812 (Homo sapiens)
Explore Q07812 
Go to UniProtKB:  Q07812
PHAROS:  Q07812
GTEx:  ENSG00000087088 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07812
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1GP
Query on 1GP

Download Ideal Coordinates CCD File 
G [auth D]SN-GLYCEROL-1-PHOSPHATE
C3 H9 O6 P
AWUCVROLDVIAJX-VKHMYHEASA-N
D12
Query on D12

Download Ideal Coordinates CCD File 
L [auth E]DODECANE
C12 H26
SNRUBQQJIBEYMU-UHFFFAOYSA-N
DD9
Query on DD9

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N [auth F]nonane
C9 H20
BKIMMITUMNQMOS-UHFFFAOYSA-N
OCT
Query on OCT

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K [auth E]N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
H [auth D],
I [auth A],
J [auth E],
M [auth E],
O [auth F]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.257 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.134α = 90
b = 83.884β = 90
c = 100.345γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia--

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-27
    Type: Initial release