2NL9

Crystal structure of the Mcl-1:Bim BH3 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural insights into the degradation of Mcl-1 induced by BH3 domains.

Czabotar, P.E.Lee, E.F.van Delft, M.F.Day, C.L.Smith, B.J.Huang, D.C.Fairlie, W.D.Hinds, M.G.Colman, P.M.

(2007) Proc.Natl.Acad.Sci.USA 104: 6217-6222

  • DOI: 10.1073/pnas.0701297104
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Apoptosis is held in check by prosurvival proteins of the Bcl-2 family. The distantly related BH3-only proteins bind to and antagonize them, thereby promoting apoptosis. Whereas binding of the BH3-only protein Noxa to prosurvival Mcl-1 induces Mcl-1 ...

    Apoptosis is held in check by prosurvival proteins of the Bcl-2 family. The distantly related BH3-only proteins bind to and antagonize them, thereby promoting apoptosis. Whereas binding of the BH3-only protein Noxa to prosurvival Mcl-1 induces Mcl-1 degradation by the proteasome, binding of another BH3-only ligand, Bim, elevates Mcl-1 protein levels. We compared the three-dimensional structures of the complexes formed between BH3 peptides of both Bim and Noxa, and we show that a discrete C-terminal sequence of the Noxa BH3 is necessary to instigate Mcl-1 degradation.


    Organizational Affiliation

    The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3050, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FUSION PROTEIN CONSISTING OF Induced myeloid leukemia cell differentiation protein Mcl-1 homolog
A
157Homo sapiensMus musculus
This entity is chimeric
Mutation(s): 0 
Gene Names: MCL1 (BCL2L3), Mcl1
Find proteins for Q07820 (Homo sapiens)
Go to Gene View: MCL1
Go to UniProtKB:  Q07820
Find proteins for P97287 (Mus musculus)
Go to UniProtKB:  P97287
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Bcl-2-like protein 11
B
26Homo sapiensMutation(s): 0 
Gene Names: BCL2L11 (BIM)
Find proteins for O43521 (Homo sapiens)
Go to Gene View: BCL2L11
Go to UniProtKB:  O43521
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.173 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 52.380α = 90.00
b = 70.080β = 90.00
c = 117.180γ = 90.00
Software Package:
Software NamePurpose
SHELXEmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-03-27
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-06-14
    Type: Source and taxonomy