Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B 

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 42.65 kDa 
• Atom Count: 2718 
• Residue Count: 330 
• Unique protein chains: 2

3IO8

BimL12F in complex with Bcl-xL

• DOI: 10.2210/pdb3IO8/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2009-08-14 Released: 2009-09-01 
• Deposition Author(s): Colman, P.M., Lee, E.F., Fairlie, W.D., Smith, B.J., Czabotar, P.E., Yang, H., Sleebs, B.E., Lessene, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.231 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 

Literature

Conformational changes in Bcl-2 pro-survival proteins determine their capacity to bind ligands.

Lee, E.F., Czabotar, P.E., Yang, H., Sleebs, B.E., Lessene, G., Colman, P.M., Smith, B.J., Fairlie, W.D.

(2009) J Biol Chem 284: 30508-30517

• PubMed: 19726685 
• DOI: 10.1074/jbc.M109.040725
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Antagonists of anti-apoptotic Bcl-2 family members hold promise as cancer therapeutics. Apoptosis is triggered when a peptide containing a BH3 motif or a small molecule BH3 peptidomimetic, such as ABT 737, binds to the relevant Bcl-2 family members. ABT-737 is an antagonist of Bcl-2, Bcl-x(L), and Bcl-w but not of Mcl-1. Here we describe new structures of mutant BH3 peptides bound to Bcl-x(L) and Mcl-1. These structures suggested a rationale for the failure of ABT-737 to bind Mcl-1, but a designed variant of ABT-737 failed to acquire binding affinity for Mcl-1. Rather, it was selective for Bcl-x(L), a result attributable in part to significant backbone refolding and movements of helical segments in its ligand binding site. To date there are few reported crystal structures of organic ligands in complex with their pro-survival protein targets. Our structure of this new organic ligand provided insights into the structural transitions that occur within the BH3 binding groove, highlighting significant differences in the structural properties of members of the Bcl-2 pro-survival protein family. Such differences are likely to influence and be important in the quest for compounds capable of selectively antagonizing the different family members.

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Organizational Affiliation: 

The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Bcl-2-like protein 1	A, C	158	Homo sapiens	Mutation(s): 0  Gene Names: BCL2L1, BCL2L, BCLX
Find proteins for Q07817 (Homo sapiens) Go to UniProtKB:  Q07817
NIH Common Fund Data Resources
PHAROS  Q07817 GTEx  ENSG00000171552

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Bcl-2-like protein 11	B, D	26	Homo sapiens	Mutation(s): 1  Gene Names: BCL2L11, BIM
Find proteins for O43521 (Homo sapiens) Go to UniProtKB:  O43521
NIH Common Fund Data Resources
PHAROS  O43521 GTEx  ENSG00000153094

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	A, C	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.231 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 
• Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.717	α = 90
b = 65.717	β = 90
c = 170.094	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-08-14 
• Released Date: 2009-09-01 
Deposition Author(s): Colman, P.M., Lee, E.F., Fairlie, W.D., Smith, B.J., Czabotar, P.E., Yang, H., Sleebs, B.E., Lessene, G.

Revision History 

• Version 1.0: 2009-09-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-07-26
  Changes: Advisory, Data collection, Refinement description, Source and taxonomy