2YV6

Crystal structure of human Bcl-2 family protein Bak


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Novel dimerization mode of the human Bcl-2 family protein Bak, a mitochondrial apoptosis regulator.

Wang, H.Takemoto, C.Akasaka, R.Uchikubo-Kamo, T.Kishishita, S.Murayama, K.Terada, T.Chen, L.Liu, Z.J.Wang, B.C.Sugano, S.Tanaka, A.Inoue, M.Kigawa, T.Shirouzu, M.Yokoyama, S.

(2009) J.Struct.Biol. 166: 32-37

  • DOI: 10.1016/j.jsb.2008.12.003

  • PubMed Abstract: 
  • Interactions of Bcl-2 family proteins play a regulatory role in mitochondrial apoptosis. The pro-apoptotic protein Bak resides in the outer mitochondrial membrane, and the formation of Bak homo- or heterodimers is involved in the regulation of apopto ...

    Interactions of Bcl-2 family proteins play a regulatory role in mitochondrial apoptosis. The pro-apoptotic protein Bak resides in the outer mitochondrial membrane, and the formation of Bak homo- or heterodimers is involved in the regulation of apoptosis. The previously reported structure of the human Bak protein (residues Glu16-Gly186) revealed that a zinc ion was coordinated with two pairs of Asp160 and His164 residues from the symmetry-related molecules. This zinc-dependent homodimer was regarded as an anti-apoptotic dimer. In the present study, we determined the crystal structure of the human Bak residues Ser23-Asn185 at 2.5A, and found a distinct type of homodimerization through Cys166 disulfide bridging between the symmetry-related molecules. In the two modes of homodimerization, the molecular interfaces are completely different. In the membrane-targeted model of the S-S bridged dimer, the BH3 motifs are too close to the membrane to interact directly with the anti-apoptotic relatives, such as Bcl-x(L). Therefore, the Bak dimer structure reported here may represent a pro-apoptotic mode under oxidized conditions.


    Organizational Affiliation

    Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bcl-2 homologous antagonist/killer
A
163Homo sapiensMutation(s): 0 
Gene Names: BAK1 (BAK, BCL2L7, CDN1)
Find proteins for Q16611 (Homo sapiens)
Go to Gene View: BAK1
Go to UniProtKB:  Q16611
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.214 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 61.824α = 90.00
b = 61.824β = 90.00
c = 137.482γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SOLVEphasing
HKL-2000data collection
HKL-2000data scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-04-15
    Type: Initial release
  • Version 1.1: 2008-10-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance