2YJ1

Puma BH3 foldamer in complex with Bcl-xL

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


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

Literature

Structural Basis of Bcl-Xl Recognition by a Bh3-Mimetic Alpha-Beta-Peptide Generated Via Sequence-Based Design

Lee, E.F., Smith, B.J., Horne, W.S., Mayer, K.N., Evangelista, M., Colman, P.M., Gellman, S.H., Fairlie, W.D.

(2011) Chembiochem 12: 2025

  • DOI: 10.1002/cbic.201100314

  • PubMed Abstract: 

    • The crystal structure of a complex between the prosurvival protein Bcl-x(L) and an α/β-peptide 21-mer is described. The α/β-peptide contains six β-amino acid residues distributed periodically throughout the sequence and adopts an α-helix-like conform ...

    The crystal structure of a complex between the prosurvival protein Bcl-x(L) and an α/β-peptide 21-mer is described. The α/β-peptide contains six β-amino acid residues distributed periodically throughout the sequence and adopts an α-helix-like conformation that mimics the bioactive shape of the Puma BH3 domain. The α/β-peptide forms all of the noncovalent contacts that have previously been identified as necessary for recognition of the prosurvival protein by an authentic BH3 domain. Comparison of our α/β-peptide:Bcl-x(L) structure with structures of complexes between native BH3 domains and Bcl-2 family proteins reveals how subtle adjustments, including variations in helix radius and helix bowing, allow the α/β-peptide to engage Bcl-x(L) with high affinity. Geometric comparisons of the BH3-mimetic α/β-peptide with α/β-peptides in helix-bundle assemblies provide insight on the conformational plasticity of backbones that contain combinations of α- and β-amino acid residues. The BH3-mimetic α/β-peptide displays prosurvival protein-binding preferences distinct from those of Puma BH3 itself, even though these two oligomers have identical side-chain sequences. Our results suggest origins for this backbone-dependent change in selectivity.

    Organizational Affiliation: 

    Structural Biology Division, The Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BCL-2-LIKE PROTEIN 1
A, C
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-PUMA BH3 FOLDAMER
B, D
23N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  8 Unique
IDChainsTypeFormula2D DiagramParent
B3E
Query on B3E
B, D
L-PEPTIDE LINKINGC6 H11 N O4GLU
B3A
Query on B3A
B, D
L-PEPTIDE LINKINGC4 H9 N O2ALA
NH2
Query on NH2
B, D
NON-POLYMERH2 N

--

B3D
Query on B3D
B, D
PEPTIDE-LIKEC5 H9 N O4ASP
HT7
Query on HT7
B, D
L-PEPTIDE LINKINGC12 H14 N2 O2TRP
HR7
Query on HR7
B, D
L-PEPTIDE LINKINGC7 H16 N4 O2ARG
B3Q
Query on B3Q
B, D
L-peptide linkingC6 H12 N2 O3

--

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

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 58.918α = 90.00
b = 71.382β = 90.00
c = 75.605γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
HKL-2000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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