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- EMDB-48602: Cryo-EM structure of a membrane transport protein -

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Basic information

Entry
Database: EMDB / ID: EMD-48602
TitleCryo-EM structure of a membrane transport protein
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: 3.23 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: 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
DepositionJan 10, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 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

Size
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

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
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_48602_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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: 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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