8GSV

Crystal structure of human BAK in complex with the Pxt1 BH3 domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for proapoptotic activation of Bak by the noncanonical BH3-only protein Pxt1.

Lim, D.Choe, S.H.Jin, S.Lee, S.Kim, Y.Shin, H.C.Choi, J.S.Oh, D.B.Kim, S.J.Seo, J.Ku, B.

(2023) PLoS Biol 21: e3002156-e3002156

  • DOI: https://doi.org/10.1371/journal.pbio.3002156
  • Primary Citation of Related Structures:  
    8GSV

  • PubMed Abstract: 

    Bak is a critical executor of apoptosis belonging to the Bcl-2 protein family. Bak contains a hydrophobic groove where the BH3 domain of proapoptotic Bcl-2 family members can be accommodated, which initiates its activation. Once activated, Bak undergoes a conformational change to oligomerize, which leads to mitochondrial destabilization and the release of cytochrome c into the cytosol and eventual apoptotic cell death. In this study, we investigated the molecular aspects and functional consequences of the interaction between Bak and peroxisomal testis-specific 1 (Pxt1), a noncanonical BH3-only protein exclusively expressed in the testis. Together with various biochemical approaches, this interaction was verified and analyzed at the atomic level by determining the crystal structure of the Bak-Pxt1 BH3 complex. In-depth biochemical and cellular analyses demonstrated that Pxt1 functions as a Bak-activating proapoptotic factor, and its BH3 domain, which mediates direct intermolecular interaction with Bak, plays a critical role in triggering apoptosis. Therefore, this study provides a molecular basis for the Pxt1-mediated novel pathway for the activation of apoptosis and expands our understanding of the cell death signaling coordinated by diverse BH3 domain-containing proteins.


  • Organizational Affiliation

    Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bcl-2 homologous antagonist/killer
A, C, E, G, I
A, C, E, G, I, K, M, O, Q, S, U, W
166Homo sapiensMutation(s): 1 
Gene Names: BAK1BAKBCL2L7CDN1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16611 (Homo sapiens)
Explore Q16611 
Go to UniProtKB:  Q16611
PHAROS:  Q16611
GTEx:  ENSG00000030110 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16611
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisomal testis-specific protein 1
B, D, F, H, J
B, D, F, H, J, L, N, P, R, T, V, X
29Homo sapiensMutation(s): 0 
Gene Names: PXT1STEPP
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NFP0 (Homo sapiens)
Explore Q8NFP0 
Go to UniProtKB:  Q8NFP0
PHAROS:  Q8NFP0
GTEx:  ENSG00000179165 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NFP0
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.215 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.997α = 120.03
b = 108.365β = 90.02
c = 108.416γ = 89.98
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2023-05-10 
  • Deposition Author(s): Lim, D., Ku, B.

Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of2019M3E5D6063955
National Research Foundation (NRF, Korea)Korea, Republic OfKGM9952213

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-10
    Type: Initial release
  • Version 1.1: 2023-06-21
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description