8H5E

Crystal structure of the MgtE TM domain in complex with Ca2+ ions at 2.5 angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Ion selectivity mechanism of the MgtE channel for Mg 2+ over Ca 2 .

Teng, X.Sheng, D.Wang, J.Yu, Y.Hattori, M.

(2022) iScience 25: 105565-105565

  • DOI: https://doi.org/10.1016/j.isci.2022.105565
  • Primary Citation of Related Structures:  
    8H5E

  • PubMed Abstract: 

    MgtE is a Mg 2+ -selective ion channel whose orthologs are widely distributed from prokaryotes to eukaryotes, including humans, and are important participants in the maintenance of cellular Mg 2+ homeostasis. The previous high-resolution structure determination of the MgtE transmembrane (TM) domain in complex with Mg 2+ ions revealed a recognition mechanism of MgtE for Mg 2+ ions. In contrast, the previous Ca 2+ -bound structure of the MgtE TM domain was determined only at moderate resolution (3.2 Å resolution), which was insufficient to visualize the water molecules coordinated to Ca 2+ ions. Here, we showed that the metal-binding site of the MgtE TM domain binds to Mg 2+ ∼500-fold more strongly than to Ca 2+ . We then determined the crystal structure of the MgtE TM domain in complex with Ca 2+ ions at a higher resolution (2.5 Å resolution), revealing hexahydrated Ca 2+ . These results provide mechanistic insights into the ion selectivity of MgtE for Mg 2+ over Ca 2+ .


  • Organizational Affiliation

    State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Key Laboratory of Bioactive Small Molecules, Department of Physiology and Neurobiology, School of Life Sciences, Fudan University, Shanghai 200438, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Magnesium transporter MgtE
A, B
183Thermus thermophilusMutation(s): 0 
Gene Names: TthHB5018_11440
Membrane Entity: Yes 
UniProt
Find proteins for Q5SMG8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SMG8 
Go to UniProtKB:  Q5SMG8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SMG8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.76α = 90
b = 70.28β = 90
c = 103.97γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China--
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-07
    Type: Initial release
  • Version 1.1: 2022-12-21
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description