3IO9

BimL12Y in complex with Mcl-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • 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. ...

    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.


    Organizational Affiliation

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Bcl-2-like protein 11
B
26Homo sapiensMutation(s): 1 
Gene Names: BCL2L11BIM
Find proteins for O43521 (Homo sapiens)
Go to UniProtKB:  O43521
NIH Common Fund Data Resources
PHAROS  O43521

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Induced myeloid leukemia cell differentiation protein Mcl-1
A
162Homo sapiensMus musculus
This entity is chimeric
Mutation(s): 0 
Gene Names: MCL1BCL2L3
Find proteins for P97287 (Mus musculus)
Go to UniProtKB:  P97287
NIH Common Fund Data Resources
IMPC  MGI:101769
Find proteins for Q07820 (Homo sapiens)
Go to UniProtKB:  Q07820
NIH Common Fund Data Resources
PHAROS  Q07820
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.537α = 90
b = 74.119β = 90
c = 117.541γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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: Refinement description, Source and taxonomy