5AGW

Bcl-2 alpha beta-1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 

Starting Model: other
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wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Alpha Beta Peptide Foldamers Targeting Intracellular Protein-Protein Interactions with Activity on Living Cells

Checco, J.W.Lee, E.F.Evangelista, M.Sleebs, N.Rodgers, K.Pettikiriarachchi, A.Kershaw, N.Eddinger, G.A.Belair, D.G.Wilson, J.L.Eller, C.H.Raines, R.T.Murphy, W.L.Smith, B.J.Gellman, S.H.Fairlie, W.D.

(2015) J Am Chem Soc 137: 11365

  • DOI: https://doi.org/10.1021/jacs.5b05896
  • Primary Citation of Related Structures:  
    5AGW, 5AGX

  • PubMed Abstract: 

    Peptides can be developed as effective antagonists of protein-protein interactions, but conventional peptides (i.e., oligomers of l-α-amino acids) suffer from significant limitations in vivo. Short half-lives due to rapid proteolytic degradation and an inability to cross cell membranes often preclude biological applications of peptides. Oligomers that contain both α- and β-amino acid residues ("α/β-peptides") manifest decreased susceptibility to proteolytic degradation, and when properly designed these unnatural oligomers can mimic the protein-recognition properties of analogous "α-peptides". This report documents an extension of the α/β-peptide approach to target intracellular protein-protein interactions. Specifically, we have generated α/β-peptides based on a "stapled" Bim BH3 α-peptide, which contains a hydrocarbon cross-link to enhance α-helix stability. We show that a stapled α/β-peptide can structurally and functionally mimic the parent stapled α-peptide in its ability to enter certain types of cells and block protein-protein interactions associated with apoptotic signaling. However, the α/β-peptide is nearly 100-fold more resistant to proteolysis than is the parent stapled α-peptide. These results show that backbone modification, a strategy that has received relatively little attention in terms of peptide engineering for biomedical applications, can be combined with more commonly deployed peripheral modifications such as side chain cross-linking to produce synergistic benefits.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
APOPTOSIS REGULATOR BCL-2, BCL-2-LIKE PROTEIN 1, APOPTOSIS REGULATOR BCL-2
A, B
166Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q07817 (Homo sapiens)
Explore Q07817 
Go to UniProtKB:  Q07817
PHAROS:  Q07817
GTEx:  ENSG00000171552 
Find proteins for P10415 (Homo sapiens)
Explore P10415 
Go to UniProtKB:  P10415
PHAROS:  P10415
GTEx:  ENSG00000171791 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ07817P10415
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
BCL-2-LIKE PROTEIN 11
C, D
22Homo sapiensMutation(s): 6 
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
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.673α = 90
b = 87.673β = 90
c = 107.48γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-09
    Type: Initial release
  • Version 1.1: 2015-09-23
    Changes: Database references
  • Version 1.2: 2019-10-23
    Changes: Data collection, Database references, Derived calculations, Other
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations
  • Version 2.1: 2024-05-01
    Changes: Refinement description