6NQ8

Crystal structure of YetJ mutant from Bacillus Subtilis - D171E


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Ion and pH Sensitivity of a TMBIM Ca2+Channel.

Guo, G.Xu, M.Chang, Y.Luyten, T.Seitaj, B.Liu, W.Zhu, P.Bultynck, G.Shi, L.Quick, M.Liu, Q.

(2019) Structure 27: 1013-1021.e3

  • DOI: 10.1016/j.str.2019.03.003
  • Primary Citation of Related Structures:  
    6NQ9, 6NQ8, 6NQ7

  • PubMed Abstract: 
  • The anti-apoptotic transmembrane Bax inhibitor motif (TMBIM) containing protein family regulates Ca 2+ homeostasis, cell death, and the progression of diseases including cancers. The recent crystal structures of the TMBIM homolog BsYetJ reveal a conserved Asp171-Asp195 dyad that is proposed in regulating a pH-dependent Ca 2+ translocation ...

    The anti-apoptotic transmembrane Bax inhibitor motif (TMBIM) containing protein family regulates Ca 2+ homeostasis, cell death, and the progression of diseases including cancers. The recent crystal structures of the TMBIM homolog BsYetJ reveal a conserved Asp171-Asp195 dyad that is proposed in regulating a pH-dependent Ca 2+ translocation. Here we show that BsYetJ mediates Ca 2+ fluxes in permeabilized mammalian cells, and its interaction with Ca 2+ is sensitive to protons and other cations. We report crystal structures of BsYetJ in additional states, revealing the flexibility of the dyad in a closed state and a pore-opening mechanism. Functional studies show that the dyad is responsible for both Ca 2+ affinity and pH dependence. Computational simulations suggest that protonation of Asp171 weakens its interaction with Arg60, leading to an open state. Our integrated analysis provides insights into the regulation of the BsYetJ Ca 2+ channel that may inform understanding of human TMBIM proteins regarding their roles in cell death and diseases.


    Organizational Affiliation

    Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA; NSLS-II, Brookhaven National Laboratory, Upton, NY 11973, USA. Electronic address: qunliu@bnl.gov.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized protein YetJA, B, C, D214Bacillus subtilis subsp. subtilis str. 168Mutation(s): 1 
Gene Names: yetJBSU07200
Membrane Entity: Yes 
UniProt
Find proteins for O31539 (Bacillus subtilis (strain 168))
Explore O31539 
Go to UniProtKB:  O31539
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 218.09α = 90
b = 117.296β = 92.97
c = 52.407γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-17
    Type: Initial release
  • Version 1.1: 2019-06-12
    Changes: Data collection, Database references