4A1U

Crystal structure of alpha-beta-foldamer 2c in complex with Bcl-xL

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 2.1 of the entry. See complete history. 

Literature

Evaluation of Diverse Alpha/Beta-Backbone Patterns for Functional Alpha-Helix Mimicry: Analogues of the Bim Bh3 Domain.

Boersma, M.D., Haase, H.S., Peterson-Kaufman, K.J., Lee, E.F., Clarke, O.B., Colman, P.M., Smith, B.J., Horne, W.S., Fairlie, W.D., Gellman, S.H.

(2012) J.Am.Chem.Soc. 134: 315

  • DOI: 10.1021/ja207148m
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Peptidic oligomers that contain both α- and β-amino acid residues, in regular patterns throughout the backbone, are emerging as structural mimics of α-helix-forming conventional peptides (composed exclusively of α-amino acid residues). Here we descri ...

    Peptidic oligomers that contain both α- and β-amino acid residues, in regular patterns throughout the backbone, are emerging as structural mimics of α-helix-forming conventional peptides (composed exclusively of α-amino acid residues). Here we describe a comprehensive evaluation of diverse α/β-peptide homologues of the Bim BH3 domain in terms of their ability to bind to the BH3-recognition sites on two partner proteins, Bcl-x(L) and Mcl-1. These proteins are members of the anti-apoptotic Bcl-2 family, and both bind tightly to the Bim BH3 domain itself. All α/β-peptide homologues retain the side-chain sequence of the Bim BH3 domain, but each homologue contains periodic α-residue → β(3)-residue substitutions. Previous work has shown that the ααβαααβ pattern, which aligns the β(3)-residues in a 'stripe' along one side of the helix, can support functional α-helix mimicry, and the results reported here strengthen this conclusion. The present study provides the first evaluation of functional mimicry by ααβ and αααβ patterns, which cause the β(3)-residues to spiral around the helix periphery. We find that the αααβ pattern can support effective mimicry of the Bim BH3 domain, as manifested by the crystal structure of an α/β-peptide bound to Bcl-x(L), affinity for a variety of Bcl-2 family proteins, and induction of apoptotic signaling in mouse embryonic fibroblast extracts. The best αααβ homologue shows substantial protection from proteolytic degradation relative to the Bim BH3 α-peptide.

    Organizational Affiliation: 

    Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BCL-2-LIKE PROTEIN 1
A
158Homo sapiensMutation(s): 0 
Gene Names: BCL2L1 (BCL2L, BCLX)
Find proteins for Q07817 (Homo sapiens)
Go to Gene View: BCL2L1
Go to UniProtKB:  Q07817
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ALPHA-BETA-FOLDAMER 2C
B
20Homo 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
SO4
Query on SO4
Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL
Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  6 Unique
IDChainsTypeFormula2D DiagramParent
B3E
Query on B3E
B
L-PEPTIDE LINKINGC6 H11 N O4GLU
B3A
Query on B3A
B
L-PEPTIDE LINKINGC4 H9 N O2ALA
NH2
Query on NH2
B
NON-POLYMERH2 N

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HT7
Query on HT7
B
L-PEPTIDE LINKINGC12 H14 N2 O2TRP
HR7
Query on HR7
B
L-PEPTIDE LINKINGC7 H16 N4 O2ARG
ACE
Query on ACE
B
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.171 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 54.706α = 90.00
b = 54.706β = 90.00
c = 119.168γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
XDSdata reduction

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-28
    Type: Initial release
  • Version 1.1: 2012-01-25
    Type: Other
  • Version 2.0: 2019-04-24
    Type: Advisory, Data collection, Derived calculations, Other, Polymer sequence
  • Version 2.1: 2019-07-10
    Type: Data collection