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- EMDB-48191: Cryo-EM structure of the magnesium transporter MgtA in an E1-like... -

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Basic information

Entry
Database: EMDB / ID: EMD-48191
TitleCryo-EM structure of the magnesium transporter MgtA in an E1-like conformation with bound Mg2+ ions
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 actuator domain / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N ...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 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 / haloacid dehalogenase-like hydrolase / 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: 3.2 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: To Be Published
Title: Cryo-EM structure of a membrane transport protein
Authors: Khan MB / Primeau JO / Basu PC / Morth JP / Lemieux MJ / Young HS
History
DepositionDec 6, 2024-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 31, 2025-
Current statusDec 31, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48191.png

Downloads & links

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Map

FileDownload / File: emd_48191.map.gz / Format: CCP4 / Size: 64 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.)
1.56 Å/pix.
x 256 pix.
= 399.898 Å		1.56 Å/pix.
x 256 pix.
= 399.898 Å		1.56 Å/pix.
x 256 pix.
= 399.898 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.5621 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0409
Minimum - Maximum-0.9880478 - 1.7579292
Average (Standard dev.)-0.000015889527 (±0.02438001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 399.8976 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_48191_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_48191_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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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: 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: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 3 / 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: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 128354
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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