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- EMDB-72125: Cryo-EM Structure of the MgtA Tetramer at 2.7 A Resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-72125
TitleCryo-EM Structure of the MgtA Tetramer at 2.7 A Resolution
Map data
Sample
  • Organelle or cellular component: P-Type ATPase
    • Protein or peptide: Magnesium-transporting ATPase, P-type 1
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: MAGNESIUM ION
  • Ligand: CARDIOLIPIN
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: 2.69 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 Mg2+-transporting P-type ATPase, MgtA.
Authors: Howard Young / Muhammad Bashir Khan / Joseph Primeau / Paramita Chaudhuri-Basu / Lucie Bergdoll / Ludovic Renault / J Preben Morth / M Joanne Lemieux
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, Mg2+ 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, Mg2+ is of critical importance in bacterial, fungal, and plant cellular homeostasis. A bacterial P-type ATPase found in Gram-negative bacteria, Mg2+ transporter A (MgtA), facilitates the transport of Mg2+ from the periplasm to the cytoplasm under conditions of Mg2+ starvation. MgtA is a cardiolipin-sensitive integral membrane ion-transporter that scavenges Mg2+ during bacterial infection and pathogenesis. Here, we determined cryo-EM structures of MgtA capturing three distinct states along the Mg2+ 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 Mg2+ in the transmembrane domain coordinated in a novel site involving Ser702 and Asn706 on M5, Ser773 and Asp777 on M7, and Ser821 and Thr824 on M8. In the E2-P conformation, the phosphate analog BeF3 is bound in close proximity to the catalytic aspartate, Asp361, suggesting that it represents a covalent aspartylphosphate intermediate. In the presence of AMPPCP, Mg2+ 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
DepositionAug 13, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72125.png

Downloads & links

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Map

FileDownload / File: emd_72125.map.gz / Format: CCP4 / Size: 303.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 430 pix.
= 399.9 Å		0.93 Å/pix.
x 430 pix.
= 399.9 Å		0.93 Å/pix.
x 430 pix.
= 399.9 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.113
Minimum - Maximum-0.33259642 - 0.7870303
Average (Standard dev.)0.00046933765 (±0.018248243)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions430430430
Spacing430430430
CellA=B=C: 399.9 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_72125_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_72125_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: DODECYL-BETA-D-MALTOSIDE
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: MAGNESIUM ION
  • Ligand: CARDIOLIPIN

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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: 4 / Enantiomer: LEVO / EC number: P-type Mg2+ transporter
Source (natural)Organism: Lactococcus lactis subsp. lactis (lactic acid bacteria)
Molecular weightTheoretical: 101.503906 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHHHL EMKKIRKTLE NTKRATTFVD NNEINARLEF AKTSTKEELF QKFKTSNKGL SEEQVEISRE QYGDNTITRG KKSSLIKRL YQAFINPFTI ILFVLALVSA FTDIILAAPG EKNPQGLIII TTMVLISGIL RFVQETRSGN AAENLLKMIT T TTNVHRLE ...String:
MHHHHHHHHL EMKKIRKTLE NTKRATTFVD NNEINARLEF AKTSTKEELF QKFKTSNKGL SEEQVEISRE QYGDNTITRG KKSSLIKRL YQAFINPFTI ILFVLALVSA FTDIILAAPG EKNPQGLIII TTMVLISGIL RFVQETRSGN AAENLLKMIT T TTNVHRLE SGSQEIPIEE VLVGDIIHLS AGDMVPADLR IIQAKDLFIS QASLTGESEP VEKLDLATAA AAASITESVN LA FMGSNVI SGSAYGVVIA TGDATIFGEM AKSVTEDSTK TTFEKGVNSV SWVLIRFMLV MVPFVLLING FTKGDWMEAA LFA LAVAVG LTPEMLPMIV TTCLAKGAVT MSKEKTIIKN LNSIQNLGSM NILCTDKTGT LTQDKVVLMR HLDIHGQENI RVLR HGFLN SYYQTGLKNL MDLAIIEGAE AKQDKNPELG GLSSKYTKVD EIPFDFERRR MSVVVKSNTN GATSKTQMIT KGAAE EMLD ICTLVEDKGN VVHLTPELRA YILKKVDELN EEGMRVILVA QKTNPSPIDT FSVQDESEMV LMGYLAFLDP PKESTA KAI KALNKYGVSV KILTGDNDKV TRSVCKQVGL PVDKTILGSD IDQLDDNELA AVAAAASVFA KLSPQQKARI VTTLRNS GN SVGYMGDGIN DAAAMKSSDV GISVDSAVDI AKESADVILL EKDLMVLEKG IIEGRKTYAN MIKYIKMTAS SNFGNMFS V LIASAFLPFI PMLSIHILLL NLIYDFSCTA IPWDNVDEEY LVVPRKWDAS SVSKFMLWIG PTSSVFDITT YLLMFFVIC PATFGPFSSL VPGSVAYIGF IALFHTGWFV ESMWTQTLVI HMIRTPKIPF LQSRASAPLT ILTFMGIIGL TIIPFTSFGH SIGLMALPI NFFPWLILTV VMYMMLVTIF KKIFVSKYGE LL

UniProtKB: Magnesium-transporting ATPase, P-type 1

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Macromolecule #2: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 2 / Number of copies: 6 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

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Macromolecule #3: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 8 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 5 / Number of copies: 17 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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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: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 105182
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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