Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 19.41 kDa 
• Atom Count: 1120 
• Modelled Residue Count: 135 
• Deposited Residue Count: 169 
• Unique protein chains: 1

4PPI

Crystal structure of Bcl-xL hexamer

• PDB DOI: 10.2210/pdb4PPI/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-02-27 Released: 2015-03-04 
• Deposition Author(s): Sreekanth, R., Yoon, H.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.269 
• R-Value Work: 0.236 
• R-Value Observed: 0.240 

Literature

Structural transition in Bcl-xL and its potential association with mitochondrial calcium ion transport

Rajan, S., Choi, M., Nguyen, Q.T., Ye, H., Liu, W., Toh, H.T., Kang, C., Kamariah, N., Li, C., Huang, H., White, C., Baek, K., Gruber, G., Yoon, H.S.

(2015) Sci Rep 5: 10609-10609

• PubMed: 26023881 
• DOI: 10.1038/srep10609
• Primary Citation of Related Structures:  
  4PPI


• PubMed Abstract: 
  

Bcl-2 family proteins are key regulators for cellular homeostasis in response to apoptotic stimuli. Bcl-xL, an antiapoptotic Bcl-2 family member, undergoes conformational transitions, which leads to two conformational states: the cytoplasmic and membrane-bound. Here we present the crystal and small-angle X-ray scattering (SAXS) structures of Bcl-xL treated with the mild detergent n-Octyl β-D-Maltoside (OM). The detergent-treated Bcl-xL forms a dimer through three-dimensional domain swapping (3DDS) by swapping helices α6-α8 between two monomers. Unlike Bax, a proapoptotic member of the Bcl-2 family, Bcl-xL is not converted to 3DDS homodimer upon binding BH3 peptides and ABT-737, a BH3 mimetic drug. We also designed Bcl-xL mutants which cannot dimerize and show that these mutants reduced mitochondrial calcium uptake in MEF cells. This illustrates the structural plasticity in Bcl-xL providing hints toward the probable molecular mechanism for Bcl-xL to play a regulatory role in mitochondrial calcium ion transport.

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Organizational Affiliation: 

1] School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551 [2] Department of Genetic Engineering, College of Life Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do, 446-701, Republic of Korea.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bcl-2-like protein 1	A	169	Homo sapiens	Mutation(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

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.269 
• R-Value Work: 0.236 
• R-Value Observed: 0.240 
• Space Group: I 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.63	α = 90
b = 153.63	β = 90
c = 153.63	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-02-27 
• Released Date: 2015-03-04 
Deposition Author(s): Sreekanth, R., Yoon, H.S.

Revision History  

• Version 1.0: 2015-03-04
  Type: Initial release
  
• Version 1.1: 2015-06-10
  Changes: Database references