Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 20.75 kDa 
• Atom Count: 1427 
• Residue Count: 164 
• Unique protein chains: 2

2YQ6

Structure of Bcl-xL bound to BimSAHB

• DOI: 10.2210/pdb2YQ6/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2012-11-06 Released: 2012-11-28 
• Deposition Author(s): Smith, B.J., Czabotar, P.E.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.201 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 

Literature

Stabilizing the Pro-Apoptotic Bimbh3 Helix (Bimsahb) Does not Necessarily Enhance Affinity or Biological Activity.

Okamoto, T., Zobel, K., Fedorova, A., Quan, C., Yang, H., Fairbrother, W.J., Huang, D.C.S., Smith, B.J., Deshayes, K., Czabotar, P.E.

(2013) ACS Chem Biol 8: 297

• PubMed: 23151250 
• DOI: 10.1021/cb3005403
• Primary Citation of Related Structures:  
  2YQ6, 2YQ7


• PubMed Abstract: 
  

An attractive approach for developing therapeutic peptides is to enhance binding to their targets by stabilizing their α-helical conformation, for example, stabilized BimBH3 peptides (BimSAHB) designed to induce apoptosis. Unexpectedly, we found that such modified peptides have reduced affinity for their targets, the pro-survival Bcl-2 proteins. We attribute this loss in affinity to disruption of a network of stabilizing intramolecular interactions present in the bound state of the native peptide. Altering this network may compromise binding affinity, as in the case of the BimBH3 stapled peptide studied here. Moreover, cells exposed to these peptides do not readily undergo apoptosis, strongly indicating that BimSAHB is not inherently cell permeable.

---

Organizational Affiliation: 

The Walter and Eliza Hall Institute of Medical Research , 1G Royal Parade, Parkville, Victoria 3052, Australia.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BCL-2-LIKE PROTEIN 1	A	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	Image
BIM BETA 5	B	19	Homo sapiens	Mutation(s): 3  Gene Names: BCL2L11, BIM
Find proteins for O43521 (Homo sapiens) Explore O43521  Go to UniProtKB:  O43521
NIH Common Fund Data Resources
PHAROS:  O43521 GTEx:  ENSG00000153094

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	A, B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MK8	B	L-PEPTIDE LINKING	C7 H15 N O2		LEU

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.201 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.736	α = 90
b = 35.336	β = 100.61
c = 61.412	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-11-06 
• Released Date: 2012-11-28 
Deposition Author(s): Smith, B.J., Czabotar, P.E.

Revision History 

• Version 1.0: 2012-11-28
  Type: Initial release
  
• Version 1.1: 2013-02-27
  Changes: Database references