Human Bcl-xL containing a Trp to Ala mutation at position 137

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.238 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


A conserved hydrophobic core at Bcl-x(L) mediates its structural stability and binding affinity with BH3-domain peptide of pro-apoptotic protein

Feng, Y.Zhang, L.Hu, T.Shen, X.Ding, J.Chen, K.Jiang, H.Liu, D.

(2009) Arch Biochem Biophys 484: 46-54

  • DOI: https://doi.org/10.1016/j.abb.2009.01.003
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Bcl-2 family proteins regulate apoptosis through their homo- and heterodimerization. By protein sequence analysis and structural comparison, we have identified a conserved hydrophobic core at the BH1 and BH2 domains of Bcl-2 family proteins. The hydrophobic core is stabilized by hydrophobic interactions among the residues of Trp137, Ile140, Trp181, Ile182, Trp188 and Phe191 in Bcl-x(L). Destabilization of the hydrophobic core can promote the protein unfolding and pore formation in synthetic lipid vesicles. Interestingly, though the hydrophobic core does not participate in binding with BH3 domain of pro-apoptotic proteins, disruption of the hydrophobic core can reduce the affinity of Bcl-x(L) with BH3-domain peptide by changing the conformation of Bcl-x(L) C-terminal residues that are involved in the peptide interaction. The BH3-domain peptide binding affinity and pore forming propensity of Bcl-x(L) were correlated to its death-repressor activity, which provides new information to help study the regulatory mechanism of anti-apoptotic proteins. Meanwhile, as the tryptophans are conserved in the hydrophobic core, in vitro binding assay based on FRET of "Trp-->AEDANS" can be devised to screen for new modulators targeting anti-apoptotic proteins as well as "multi-BH domains" pro-apoptotic proteins.

  • Organizational Affiliation

    Department of Molecular Pharmacology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu-Chong-Zhi Road, Shanghai 201203, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Apoptosis regulator Bcl-XA [auth X]219Homo sapiensMutation(s): 1 
Gene Names: bcl-xl
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
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.238 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.828α = 90
b = 61.828β = 90
c = 111.745γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-03-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2021-11-10
    Changes: Database references
  • Version 1.4: 2023-11-01
    Changes: Data collection, Refinement description