4QVE

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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
  • Primary Citation of Related Structures:  

  • 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

    School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.




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
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Peptide from BH3-interacting domain death agonist
B
34Homo sapiensMutation(s): 0 
Gene Names: BID
Find proteins for P55957 (Homo sapiens)
Go to Gene View: BID
Go to UniProtKB:  P55957
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IMD
Query on IMD

Download SDF File 
Download CCD File 
B
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.179 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 63.760α = 90.00
b = 63.760β = 90.00
c = 187.652γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
ADSCdata collection
MOSFLMdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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