Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 41.07 kDa 
• Atom Count: 2761 
• Residue Count: 335 
• Unique protein chains: 2

2YJ1

Puma BH3 foldamer in complex with Bcl-xL

• DOI: 10.2210/pdb2YJ1/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-05-18 Released: 2011-10-12 
• Deposition Author(s): Lee, E.F., Smith, B.J., Horne, W.S., Mayer, K.N., Evangelista, M., Colman, P.M., Gellman, S.H., Fairlie, W.D.

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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 

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

• PubMed: 21744457 
• DOI: 10.1002/cbic.201100314
• Structures With Same Primary Citation


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
BCL-2-LIKE PROTEIN 1	A, C	158	Homo sapiens	Mutation(s): 0  Gene Names: BCL2L1, BCL2L, BCLX
Find proteins for Q07817 (Homo sapiens) Explore Q07817  Go to UniProtKB:  Q07817
NIH Common Fund Data Resources
PHAROS  Q07817 GTEx  ENSG00000171552

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
ALPHA-BETA-PUMA BH3 FOLDAMER	B, D	23	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  5 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
B3A	B,D	L-PEPTIDE LINKING	C4 H9 N O2		ALA
B3D	B,D	PEPTIDE-LIKE	C5 H9 N O4		ASP
B3E	B,D	L-PEPTIDE LINKING	C6 H11 N O4		GLU
HR7	B,D	L-PEPTIDE LINKING	C7 H16 N4 O2		ARG
HT7	B,D	L-PEPTIDE LINKING	C12 H14 N2 O2		TRP

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 = 58.918	α = 90
b = 71.382	β = 90
c = 75.605	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-05-18 
• Released Date: 2011-10-12 
Deposition Author(s): Lee, E.F., Smith, B.J., Horne, W.S., Mayer, K.N., Evangelista, M., Colman, P.M., Gellman, S.H., Fairlie, W.D.

Revision History 

• 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