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- EMDB-48602: Cryo-EM Structure of the Magnesium Transporter MgtA in the E2 Con... -

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Basic information

Entry
Database: EMDB / ID: EMD-48602
TitleCryo-EM Structure of the Magnesium Transporter MgtA in the E2 Conformation Bound to Mg2+
Map data
Sample
  • Organelle or cellular component: P-Type ATPase
    • Protein or peptide: Magnesium-transporting ATPase, P-type 1
  • Ligand: MAGNESIUM ION
KeywordsP-type ATPase / Metal Transport / TRANSPORT PROTEIN
Function / homology
Function and homology information


P-type Mg2+ transporter / P-type magnesium transporter activity / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
P-type ATPase, subfamily IIIB / Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / P-type ATPase, cytoplasmic domain N / : / P-type ATPase actuator domain / P-type ATPase, haloacid dehalogenase domain ...P-type ATPase, subfamily IIIB / Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / P-type ATPase, cytoplasmic domain N / : / P-type ATPase actuator domain / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Magnesium-transporting ATPase, P-type 1
Similarity search - Component
Biological speciesLactococcus lactis subsp. lactis (lactic acid bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsKhan MB / Primeau JO / Basu PC / Morth JP / Lemieux MJ / Young HS
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Res Sq / Year: 2026
Title: Distinct transport cycle and lipid regulation of a Mg-transporting P-type ATPase, MgtA.
Authors: Muhammad Bashir Khan / Joseph O Primeau / Paramita Chaudhuri-Basu / Lucie Bergdoll / Ludovic Renault / Jens Preben Morth / M Joanne Lemieux / Howard S Young /
Abstract: P-type ATPases represent an evolutionarily conserved superfamily of ion, lipid, and peptide pumps found across all domains of life. Among the substrates transported by P-type ATPases, Mg is of ...P-type ATPases represent an evolutionarily conserved superfamily of ion, lipid, and peptide pumps found across all domains of life. Among the substrates transported by P-type ATPases, Mg is of critical importance in bacterial, fungal, and plant cellular homeostasis. A bacterial P-type ATPase found in Gram-negative bacteria, Mg transporter A (MgtA), facilitates the transport of Mg from the periplasm to the cytoplasm under conditions of Mg starvation. MgtA is a cardiolipin-sensitive integral membrane ion-transporter that scavenges Mg during bacterial infection and pathogenesis. Here, we determined cryo-EM structures of MgtA capturing three distinct states along the Mg transport cycle, including a phosphorylated E2-P intermediate (2.6 Å resolution), an E1-like conformation stabilized by the peptide regulator MgtR (2.7 Å resolution), and an E1-like ATP-bound state (2.8 Å resolution). These three conformations reveal the binding of Mg in the transmembrane domain coordinated in a novel site involving Ser and Asn on M5, Ser and Asp on M7, and Ser and Thr on M8. In the E2-P conformation, the phosphate analog BeF is bound in close proximity to the catalytic aspartate, Asp, suggesting that it represents a covalent aspartylphosphate intermediate. In the presence of AMPPCP, Mg remains bound in the transmembrane domain and the ATP analog is bound in a catalytically competent conformation. Overall, the structures reveal distinct steps in the transport cycle of MgtA compared to other P-type ATPases, as well as lipid binding sites that fill gaps in our understanding of transport regulation.
History
DepositionJan 10, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48602.png

Downloads & links

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Map

FileDownload / File: emd_48602.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 300 pix.
= 279. Å		0.93 Å/pix.
x 300 pix.
= 279. Å		0.93 Å/pix.
x 300 pix.
= 279. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.29793411 - 0.6512863
Average (Standard dev.)0.0005218819 (±0.01397963)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 279.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_48602_half_map_1.map
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Half map: #2

Fileemd_48602_half_map_2.map
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Sample components

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Entire : P-Type ATPase

EntireName: P-Type ATPase
Components
  • Organelle or cellular component: P-Type ATPase
    • Protein or peptide: Magnesium-transporting ATPase, P-type 1
  • Ligand: MAGNESIUM ION

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Supramolecule #1: P-Type ATPase

SupramoleculeName: P-Type ATPase / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Lactococcus lactis subsp. lactis (lactic acid bacteria)

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Macromolecule #1: Magnesium-transporting ATPase, P-type 1

MacromoleculeName: Magnesium-transporting ATPase, P-type 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: P-type Mg2+ transporter
Source (natural)Organism: Lactococcus lactis subsp. lactis (lactic acid bacteria)
Molecular weightTheoretical: 99.350258 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHHHL EDNNEINARL EFAKTSTKEE LFQKFKTSNK GLSEEQVEIS REQYGDNTIT RGKKSSLIKR LYQAFINPFT IILFVLALV SAFTDIILAA PGEKNPQGLI IITTMVLISG ILRFVQETRS GNAAENLLKM ITTTTNVHRL ESGSQEIPIE E VLVGDIIH ...String:
MHHHHHHHHL EDNNEINARL EFAKTSTKEE LFQKFKTSNK GLSEEQVEIS REQYGDNTIT RGKKSSLIKR LYQAFINPFT IILFVLALV SAFTDIILAA PGEKNPQGLI IITTMVLISG ILRFVQETRS GNAAENLLKM ITTTTNVHRL ESGSQEIPIE E VLVGDIIH LSAGDMVPAD LRIIQAKDLF ISQASLTGES EPVEKLDLAT AAAAASITES VNLAFMGSNV ISGSAYGVVI AT GDATIFG EMAKSVTEDS TKTTFEKGVN SVSWVLIRFM LVMVPFVLLI NGFTKGDWME AALFALAVAV GLTPEMLPMI VTT CLAKGA VTMSKEKTII KNLNSIQNLG SMNILCTDKT GTLTQDKVVL MRHLDIHGQE NIRVLRHGFL NSYYQTGLKN LMDL AIIEG AEAKQDKNPE LGGLSSKYTK VDEIPFDFER RRMSVVVKSN TNGATSKTQM ITKGAAEEML DICTLVEDKG NVVHL TPEL RAYILKKVDE LNEEGMRVIL VAQKTNPSPI DTFSVQDESE MVLMGYLAFL DPPKESTAKA IKALNKYGVS VKILTG DND KVTRSVCKQV GLPVDKTILG SDIDQLDDNE LAAVAAAASV FAKLSPQQKA RIVTTLRNSG NSVGYMGDGI NDAAAMK SS DVGISVDSAV DIAKESADVI LLEKDLMVLE KGIIEGRKTY ANMIKYIKMT ASSNFGNMFS VLIASAFLPF IPMLSIHI L LLNLIYDFSC TAIPWDNVDE EYLVVPRKWD ASSVSKFMLW IGPTSSVFDI TTYLLMFFVI CPATFGPFSS LVPGSVAYI GFIALFHTGW FVESMWTQTL VIHMIRTPKI PFLQSRASAP LTILTFMGII GLTIIPFTSF GHSIGLMALP INFFPWLILT VVMYMMLVT IFKKIFVSKY GELL

UniProtKB: Magnesium-transporting ATPase, P-type 1

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration14 mg/mL
BufferpH: 7.5
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 138397
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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