6NQ7

Crystal structure of YetJ from Bacillus Subtilis crystallized in lipidic cubic phase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.243 

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:  
    6NQ7, 6NQ8, 6NQ9

  • 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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized protein YetJA209Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: yetJBSU07200
Membrane Entity: Yes 
UniProt
Find proteins for O31539 (Bacillus subtilis (strain 168))
Explore O31539 
Go to UniProtKB:  O31539
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO31539
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GD
Query on GD

Download Ideal Coordinates CCD File 
B [auth A]GADOLINIUM ATOM
Gd
UIWYJDYFSGRHKR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.243 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.864α = 90
b = 63.037β = 93.95
c = 47.336γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
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