3IO9 | pdb_00003io9

BimL12Y in complex with Mcl-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.251 (Depositor), 0.268 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3IO9

This is version 1.4 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 Biological Chem 284: 30508-30517

  • DOI: https://doi.org/10.1074/jbc.M109.040725
  • Primary Citation Related Structures: 
    3INQ, 3IO8, 3IO9

  • 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.


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

Macromolecule Content 

  • Total Structure Weight: 21.81 kDa 
  • Atom Count: 1,423 
  • Modeled Residue Count: 165 
  • Deposited Residue Count: 188 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Induced myeloid leukemia cell differentiation protein Mcl-1162Homo sapiensMus musculus
This entity is chimeric
Mutation(s): 0 
Gene Names: MCL1BCL2L3Mcl1
UniProt & NIH Common Fund Data Resources
Find proteins for P97287 (Mus musculus)
Explore P97287 
Go to UniProtKB:  P97287
IMPC:  MGI:101769
Find proteins for Q07820 (Homo sapiens)
Explore Q07820 
Go to UniProtKB:  Q07820
PHAROS:  Q07820
GTEx:  ENSG00000143384 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP97287Q07820
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Bcl-2-like protein 1126Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for O43521 (Homo sapiens)
Explore O43521 
Go to UniProtKB:  O43521
PHAROS:  O43521
GTEx:  ENSG00000153094 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43521
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.251 (Depositor), 0.268 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
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

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2021-10-13
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-09-06
    Changes: Data collection, Refinement description