Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 20.86 kDa 
• Atom Count: 1246 
• Modelled Residue Count: 161 
• Deposited Residue Count: 187 
• Unique protein chains: 2

4ZIH

Crystal Structure of core/latch dimer of Bax in complex with BimBH3mini

• PDB DOI: 10.2210/pdb4ZIH/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-04-28 Released: 2015-07-22 
• Deposition Author(s): Robin, A.Y., Krishna Kumar, K., Westphal, D., Wardak, A.Z., Thompson, G.V., Dewson, G., Colman, P.M., Czabotar, P.E.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.233 
• R-Value Work: 0.186 
• R-Value Observed: 0.189 

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

• PubMed: 26158515 
• 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 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.

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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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Apoptosis regulator BAX	A	167	Homo sapiens	Mutation(s): 2  Gene Names: BAX, BCL2L4
UniProt & NIH Common Fund Data Resources
Find proteins for Q07812 (Homo sapiens) Explore Q07812  Go to UniProtKB:  Q07812
PHAROS:  Q07812 GTEx:  ENSG00000087088

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Bcl-2-like protein 11	B	20	Homo sapiens	Mutation(s): 0  Gene Names: BCL2L11, BIM
UniProt & NIH Common Fund Data Resources
Find proteins for O43521 (Homo sapiens) Explore O43521  Go to UniProtKB:  O43521
PHAROS:  O43521 GTEx:  ENSG00000153094

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.233 
• R-Value Work: 0.186 
• R-Value Observed: 0.189 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.73	α = 90
b = 95.73	β = 90
c = 37.1	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-04-28 
• Released Date: 2015-07-22 
Deposition Author(s): Robin, A.Y., Krishna Kumar, K., Westphal, D., Wardak, A.Z., Thompson, G.V., Dewson, G., Colman, P.M., Czabotar, P.E.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	Projects Grant 1079706
National Health and Medical Research Council (NHMRC, Australia)	Australia	Projects Grant 1059331
National Health and Medical Research Council (NHMRC, Australia)	Australia	Projects Grant 1023055
National Health and Medical Research Council (NHMRC, Australia)	Australia	Program 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