Macromolecule Content

• Total Structure Weight: 21.59 kDa 
• Atom Count: 1521 
• Residue Count: 189 
• Unique protein chains: 2

2ROC

Solution structure of Mcl-1 Complexed with Puma

• DOI: 10.2210/pdb2ROC/pdb

• Classification: APOPTOSIS
• Mutation(s): Yes 


• Deposited: 2008-03-17 Released: 2008-07-08 
• Deposition Author(s): Day, C.L., Smits, C., Fan, F.C., Lee, E.F., Fairlie, W.D., Hinds, M.G.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 256 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations 

Literature

Structure of the BH3 Domains from the p53-Inducible BH3-Only Proteins Noxa and Puma in Complex with Mcl-1

Day, C.L., Smits, C., Fan, F.C., Lee, E.F., Fairlie, W.D., Hinds, M.G.

(2008) J Mol Biol 380: 958-971

• PubMed: 18589438 
• DOI: 10.1016/j.jmb.2008.05.071
• Primary Citation of Related Structures:  
  2ROD, 2ROC


• PubMed Abstract: 
  

Pro-survival proteins in the B-cell lymphoma-2 (Bcl-2) family have a defined specificity profile for their cell death-inducing BH3-only antagonists. Solution structures of myeloid cell leukaemia-1 (Mcl-1) in complex with the BH3 domains from Noxa and Puma, two proteins regulated by the tumour suppressor p53, show that they bind as amphipathic alpha-helices in the same hydrophobic groove of Mcl-1, using conserved residues for binding. Thermodynamic parameters for the interaction of Noxa, Puma and the related BH3 domains of Bmf, Bim, Bid and Bak with Mcl-1 were determined by calorimetry. These unstructured BH3 domains bind Mcl-1 with affinities that span 3 orders of magnitude, and binding is an enthalpically driven and entropy-enthalpy-compensated process. Alanine scanning analysis of Noxa demonstrated that only a subset of residues is required for interaction with Mcl-1, and these residues are localised to a short highly conserved sequence motif that defines the BH3 domain. Chemical shift mapping of Mcl-1:BH3 complexes showed that Mcl-1 engages all BH3 ligands in a similar way and that, in addition to changes in the immediate vicinity of the binding site, small molecule-wide structural adjustments accommodate ligand binding. Our studies show that unstructured peptides, such as the BH3 domains, behave like their structured counterparts and can bind tightly and selectively in an enthalpically driven process.

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Organizational Affiliation: 

Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Induced myeloid leukemia cell differentiation protein Mcl-1 homolog	A	162	N/A	Mutation(s): 0  Gene Names: Mcl-1
Find proteins for P97287 (Mus musculus) Explore P97287  Go to UniProtKB:  P97287
NIH Common Fund Data Resources
IMPC  MGI:101769

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Bcl-2-binding component 3	B	27	N/A	Mutation(s): 1  Gene Names: Puma
Find proteins for Q99ML1 (Mus musculus) Explore Q99ML1  Go to UniProtKB:  Q99ML1
NIH Common Fund Data Resources
IMPC  MGI:2181667

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 256 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations 
• OLDERADO: 2ROC Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-03-17 
• Released Date: 2008-07-08 
Deposition Author(s): Day, C.L., Smits, C., Fan, F.C., Lee, E.F., Fairlie, W.D., Hinds, M.G.

Revision History 

• Version 1.0: 2008-07-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance