5AGX

Bcl-2 alpha beta-1 LINEAR complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1021/jacs.5b05896
  • Primary Citation of Related Structures:  

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
APOPTOSIS REGULATOR BCL-2, BCL-2-LIKE PROTEIN 1, APOPTOSIS REGULATOR BCL-2
A
166Homo sapiensMutation(s): 0 
Gene Names: BCL2, BCL2L1 (BCL2L, BCLX)
Find proteins for P10415 (Homo sapiens)
Go to Gene View: BCL2
Go to UniProtKB:  P10415
Find proteins for Q07817 (Homo sapiens)
Go to Gene View: BCL2L1
Go to UniProtKB:  Q07817
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
APOPTOSIS REGULATOR BCL-2, BCL-2-LIKE PROTEIN 1, APOPTOSIS REGULATOR BCL-2
B
166Homo sapiensMutation(s): 0 
Gene Names: BCL2, BCL2L1 (BCL2L, BCLX)
Find proteins for P10415 (Homo sapiens)
Go to Gene View: BCL2
Go to UniProtKB:  P10415
Find proteins for Q07817 (Homo sapiens)
Go to Gene View: BCL2L1
Go to UniProtKB:  Q07817
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
BCL-2-LIKE PROTEIN 11
C, D
22Homo sapiensMutation(s): 5 
Gene Names: BCL2L11 (BIM)
Find proteins for O43521 (Homo sapiens)
Go to Gene View: BCL2L11
Go to UniProtKB:  O43521
Small Molecules
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
AJE
Query on AJE
C, D
L-PEPTIDE LINKINGC9 H14 N2 O5

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MH8
Query on MH8
C, D
L-peptide linkingC8 H15 N O2

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XCP
Query on XCP
C, D
peptide-likeC6 H11 N O2

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ACE
Query on ACE
C, D
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.188 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 86.054α = 90.00
b = 86.054β = 90.00
c = 108.739γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-09
    Type: Initial release
  • Version 1.1: 2015-09-23
    Type: Database references