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 4PPI | pdb_00004ppi

Crystal structure of Bcl-xL hexamer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 
    0.269 (Depositor), 0.278 (DCC) 
  • R-Value Work: 
    0.236 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 
    0.240 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4PPI

This is version 1.2 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: https://doi.org/10.1038/srep10609
  • Primary Citation 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.


  • Organizational Affiliation: 
    • School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551.

Macromolecule Content 

  • Total Structure Weight: 19.41 kDa 
  • Atom Count: 1,120 
  • Modeled Residue Count: 135 
  • Deposited Residue Count: 169 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Bcl-2-like protein 1169Homo 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
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

Query on GOL



Download:Ideal Coordinates CCD File
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 (Depositor), 0.278 (DCC) 
  • R-Value Work:  0.236 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.240 (Depositor) 
Space Group: I 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.63α = 90
b = 153.63β = 90
c = 153.63γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-04
    Type: Initial release
  • Version 1.1: 2015-06-10
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description