4ZII

Crystal Structure of core/latch dimer of BaxI66A in complex with BidBH3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of Bax bound to the BH3 peptide of Bim identifies important contacts for interaction.

Robin, A.Y.Krishna Kumar, K.Westphal, D.Wardak, A.Z.Thompson, G.V.Dewson, G.Colman, P.M.Czabotar, P.E.

(2015) Cell Death Dis 6: e1809-e1809

  • DOI: 10.1038/cddis.2015.141
  • Primary Citation of Related Structures:  
    4ZIE, 4ZIF, 4ZIG, 4ZIH, 4ZII

  • PubMed Abstract: 
  • The BH3-only protein Bim is a potent direct activator of the proapoptotic effector protein Bax, but the structural basis for its activity has remained poorly defined. Here we describe the crystal structure of the BimBH3 peptide bound to BaxΔC26 and s ...

    The BH3-only protein Bim is a potent direct activator of the proapoptotic effector protein Bax, but the structural basis for its activity has remained poorly defined. Here we describe the crystal structure of the BimBH3 peptide bound to BaxΔC26 and structure-based mutagenesis studies. Similar to BidBH3, the BimBH3 peptide binds into the cognate surface groove of Bax using the conserved hydrophobic BH3 residues h1-h4. However, the structure and mutagenesis data show that Bim is less reliant compared with Bid on its 'h0' residues for activating Bax and that a single amino-acid difference between Bim and Bid encodes a fivefold difference in Bax-binding potency. Similar to the structures of BidBH3 and BaxBH3 bound to BaxΔC21, the structure of the BimBH3 complex with BaxΔC displays a cavity surrounded by Bax α1, α2, α5 and α8. Our results are consistent with a model in which binding of an activator BH3 domain to the Bax groove initiates separation of its core (α2-α5) and latch (α6-α8) domains, enabling its subsequent dimerisation and the permeabilisation of the mitochondrial outer membrane.


    Organizational Affiliation

    1] The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia [2] Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Apoptosis regulator BAXA170Homo sapiensMutation(s): 2 
Gene Names: BAXBCL2L4
Find proteins for Q07812 (Homo sapiens)
Explore Q07812 
Go to UniProtKB:  Q07812
NIH Common Fund Data Resources
PHAROS  Q07812
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
BH3-interacting domain death agonistC34Homo sapiensMutation(s): 0 
Gene Names: BID
Find proteins for P55957 (Homo sapiens)
Explore P55957 
Go to UniProtKB:  P55957
NIH Common Fund Data Resources
PHAROS  P55957
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.180 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.801α = 90
b = 103.801β = 90
c = 38.007γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)AustraliaProjects Grant 1079706
National Health and Medical Research Council (NHMRC, Australia)AustraliaProjects Grant 1059331
National Health and Medical Research Council (NHMRC, Australia)AustraliaProjects Grant 1023055
National Health and Medical Research Council (NHMRC, Australia)AustraliaProgram Grant 1016701

Revision History 

  • Version 1.0: 2015-07-22
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Author supporting evidence, Data collection, Derived calculations, Source and taxonomy
  • Version 1.2: 2020-01-08
    Changes: Author supporting evidence