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 
  • R-Value Observed: 0.194 

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
  • Primary Citation of Related Structures:  
    2YJ1

  • 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 conformation that mimics the bioactive shape of the Puma BH3 domain ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BCL-2-LIKE PROTEIN 1A, C158Homo sapiensMutation(s): 0 
Gene Names: BCL2L1, BCL2L, BCLX
UniProt & NIH Common Fund Data Resources
Find proteins for Q07817 (Homo sapiens)
Explore Q07817 
Go to UniProtKB:  Q07817
PHAROS:  Q07817
GTEx:  ENSG00000171552 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07817
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ALPHA-BETA-PUMA BH3 FOLDAMERB, D23synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  5 Unique
IDChainsTypeFormula2D DiagramParent
B3A
Query on B3A		B, D L-PEPTIDE LINKINGC4 H9 N O2ALA
B3D
Query on B3D		B, D PEPTIDE-LIKEC5 H9 N O4ASP
B3E
Query on B3E		B, D L-PEPTIDE LINKINGC6 H11 N O4GLU
HR7
Query on HR7		B, D L-PEPTIDE LINKINGC7 H16 N4 O2ARG
HT7
Query on HT7		B, D L-PEPTIDE LINKINGC12 H14 N2 O2TRP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.918α = 90
b = 71.382β = 90
c = 75.605γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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