8XHW | pdb_00008xhw

Haloquadratum walsbyi middle rhodopsin mutant - D84N


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free: 
    0.273 (Depositor), 0.273 (DCC) 
  • R-Value Work: 
    0.239 (Depositor), 0.239 (DCC) 
  • R-Value Observed: 
    0.243 (Depositor) 

Starting Model: in silico
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Rhodopsin from Haloquadratum walsbyi is a light-driven magnesium transporter.

Ko, L.N.Lim, G.Z.Chen, J.C.Ko, T.Li, G.Y.Yang, C.S.

(2025) Nat Commun 16: 4472-4472

  • DOI: https://doi.org/10.1038/s41467-025-59795-y
  • Primary Citation of Related Structures:  
    8XHW, 9JWS

  • PubMed Abstract: 

    The functionally unknown Middle rhodopsin (HwMR) is a microbial rhodopsin (mRho) identified in Haloquadratum walsbyi, an archaeon that thrives in a 2 M MgCl 2 environment harmful to most other microorganisms. HwMR shares conserved and functionally critical residues with both bacteriorhodopsin (BR), a proton pump, and sensory rhodopsin II (SRII), which mediates phototaxis, even though HwMR exerts neither function. We previously reported HwMR as a unique mRho found to associate with Mg 2+ . Here, we show that HwMR can sense environmental Mg 2+ concentration via the D84 residue according to characteristic maximum absorption wavelength shift, photocycle kinetics, and Mg 2+ titration assay. X-ray crystallography of the wild-type HwMR and its D84N mutant produced two HwMR atomic structure models. Omit maps analysis of the wild-type HwMR model revealed D84 as a Mg 2+ binding site. On the cytoplasmic side, omit maps also revealed Mg 2+ association with T216. Both Mg 2+ sites were absent in the D84N mutant. A cell-based light-driven conductivity assay provided evidence to propose that HwMR is an inward magnesium transporter, with D84 as the primary binding site and T216 as the transportation stabilizing site. A sequential model was proposed to illustrate Mg 2+ transportation in HwMR.


  • Organizational Affiliation
    • Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei, Taiwan, ROC.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bacteriorhodopsin-II-like protein
A, B, C, D
246Haloquadratum walsbyi DSM 16790Mutation(s): 1 
Gene Names: bop2bopIIHQ_1017A
Membrane Entity: Yes 
UniProt
Find proteins for Q18DH5 (Haloquadratum walsbyi (strain DSM 16790 / HBSQ001))
Explore Q18DH5 
Go to UniProtKB:  Q18DH5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ18DH5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free:  0.273 (Depositor), 0.273 (DCC) 
  • R-Value Work:  0.239 (Depositor), 0.239 (DCC) 
  • R-Value Observed: 0.243 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.366α = 90
b = 61.367β = 93.95
c = 118.793γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-18
    Type: Initial release
  • Version 1.1: 2025-05-28
    Changes: Database references