4WIB | pdb_00004wib

Crystal structure of Magnesium transporter MgtE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.268 (Depositor), 0.237 (DCC) 
  • R-Value Work: 
    0.240 (Depositor), 0.259 (DCC) 
  • R-Value Observed: 
    0.242 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structural basis for ion selectivity revealed by high-resolution crystal structure of Mg(2+) channel MgtE

Takeda, H.Hattori, M.Nishizawa, T.Yamashita, K.Shah, S.T.Caffrey, M.Maturana, A.D.Ishitani, R.Nureki, O.

(2014) Nat Commun 5: 5374-5374

  • DOI: https://doi.org/10.1038/ncomms6374
  • Primary Citation Related Structures: 
    4U9L, 4U9N, 4WIB

  • PubMed Abstract: 

    Magnesium is the most abundant divalent cation in living cells and is crucial to several biological processes. MgtE is a Mg(2+) channel distributed in all domains of life that contributes to the maintenance of cellular Mg(2+) homeostasis. Here we report the high-resolution crystal structures of the transmembrane domain of MgtE, bound to Mg(2+), Mn(2+) and Ca(2+). The high-resolution Mg(2+)-bound crystal structure clearly visualized the hydrated Mg(2+) ion within its selectivity filter. Based on those structures and biochemical analyses, we propose a cation selectivity mechanism for MgtE in which the geometry of the hydration shell of the fully hydrated Mg(2+) ion is recognized by the side-chain carboxylate groups in the selectivity filter. This is in contrast to the K(+)-selective filter of KcsA, which recognizes a dehydrated K(+) ion. Our results further revealed a cation-binding site on the periplasmic side, which regulate channel opening and prevents conduction of near-cognate cations.


  • Organizational Affiliation
    • 1] Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan [2] Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.

Macromolecule Content 

  • Total Structure Weight: 38.58 kDa 
  • Atom Count: 2,610 
  • Modeled Residue Count: 356 
  • Deposited Residue Count: 356 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Magnesium transporter MgtE
A, B
178Thermus thermophilus HB8Mutation(s): 0 
Gene Names: TTHA1060
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: 3.20 Å
  • R-Value Free:  0.268 (Depositor), 0.237 (DCC) 
  • R-Value Work:  0.240 (Depositor), 0.259 (DCC) 
  • R-Value Observed: 0.242 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.12α = 90
b = 70.38β = 90
c = 103.34γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-03
    Type: Initial release
  • Version 1.1: 2020-02-05
    Changes: Data collection, Derived calculations, Other, Source and taxonomy, Structure summary
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references, Derived calculations, Refinement description