4PPI

Crystal structure of Bcl-xL hexamer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.851 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1038/srep10609

  • 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 memb ...

    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.


    Organizational Affiliation

    Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Singapore 138671.,Department of Physiology and Biophysics, Rosalind Franklin University of Medicine and Science, 3333 Green Bay Road, North Chicago, IL 60064, USA.,Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), Singapore 138669.,1] School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551 [2] Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Singapore 138671.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551.,Molecular Targets Program, James Graham Brown Center and Department of Medicine, Pharmacology and Toxicology, University of Louisville, Louisville, KY 40202, USA.,Department of Genetic Engineering, College of Life Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do, 446-701, Republic of Korea.,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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bcl-2-like protein 1
A
169Homo sapiensMutation(s): 0 
Gene Names: BCL2L1 (BCL2L, BCLX)
Find proteins for Q07817 (Homo sapiens)
Go to Gene View: BCL2L1
Go to UniProtKB:  Q07817
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.851 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.236 
  • Space Group: I 41 3 2
Unit Cell:
Length (Å)Angle (°)
a = 153.630α = 90.00
b = 153.630β = 90.00
c = 153.630γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
PHENIXrefinement
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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