4QVF

Crystal structure of Bcl-xL in complex with BIM BH3 domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.167 

wwPDB Validation 3D Report Full Report



Literature

Bh3 induced conformational changes in Bcl-Xl revealed by crystal structure and comparative analysis

Rajan, S.Choi, M.Baek, K.Yoon, H.S.

(2015) Proteins 

  • DOI: 10.1002/prot.24816
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Apoptosis or programmed cell death is a regulatory process in cells in response to stimuli perturbing physiological conditions. The Bcl-2 family of proteins plays an important role in regulating homeostasis during apoptosis. In the process, the molec ...

    Apoptosis or programmed cell death is a regulatory process in cells in response to stimuli perturbing physiological conditions. The Bcl-2 family of proteins plays an important role in regulating homeostasis during apoptosis. In the process, the molecular interactions among the three members of this family, the pro-apoptotic, anti-apoptotic and BH3-only proteins at the mitochondrial outer membrane define the fate of a cell. Here, we report the crystal structures of the human anti-apoptotic protein Bcl-XL in complex with BH3-only BID(BH3) and BIM(BH3) peptides determined at 2.0 Å and 1.5 Å resolution, respectively. The BH3 peptides bind to the canonical hydrophobic pocket in Bcl-XL and adopt an alpha helical conformation in the bound form. Despite a similar structural fold, a comparison with other BH3 complexes revealed structural differences due to their sequence variations. In the Bcl-XL-BID(BH3) complex we observed a large pocket, in comparison with other BH3 complexes, lined by residues from helices α1, α2, α3, and α5 located adjacent to the canonical hydrophobic pocket. These results suggest that there are differences in the mode of interactions by the BH3 peptides that may translate into functional differences in apoptotic regulation.


    Organizational Affiliation

    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: BCL2L1BCL2LBCLX
Find proteins for Q07817 (Homo sapiens)
Go to UniProtKB:  Q07817
NIH Common Fund Data Resources
PHAROS  Q07817

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Peptide from Bcl-2-like protein 11
B
26Homo sapiensMutation(s): 0 
Gene Names: BCL2L11BIM
Find proteins for O43521 (Homo sapiens)
Go to UniProtKB:  O43521
NIH Common Fund Data Resources
PHAROS  O43521
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.167 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.54α = 90
b = 47.95β = 105.03
c = 34.18γ = 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 

  • Version 1.0: 2015-06-10
    Type: Initial release