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- EMDB-45025: Cryo-EM structure of a membrane transport protein -

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Basic information

Entry
Database: EMDB / ID: EMD-45025
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
  • Ligand: CARDIOLIPIN
KeywordsP-type ATPase / METAL TRANSPORT
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 CV56 (lactic acid bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.29 Å
AuthorsKhan MB / Primeau JO / 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 / Young HS
History
DepositionMay 23, 2024-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45025.png

Downloads & links

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Map

FileDownload / File: emd_45025.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.79 Å/pix.
x 450 pix.
= 354.6 Å		0.79 Å/pix.
x 450 pix.
= 354.6 Å		0.79 Å/pix.
x 450 pix.
= 354.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.788 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00997
Minimum - Maximum-0.09942383 - 0.17122073
Average (Standard dev.)0.000052459713 (±0.0031253714)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 354.6 Å
α=β=γ: 90.0 °

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Supplemental data

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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
  • 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 CV56 (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: 2 / Enantiomer: LEVO / EC number: P-type Mg2+ transporter
Source (natural)Organism: Lactococcus lactis subsp. lactis CV56 (lactic acid bacteria)
Molecular weightTheoretical: 99.350258 KDa
Recombinant expressionOrganism: Escherichia coli O103:H2 str. 12009 (bacteria)
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: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #3: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 3 / Number of copies: 2 / 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

BufferpH: 7.5
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 150.0 µm / Calibrated defocus min: 0.27 µm / Illumination 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: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.29 Å / Resolution method: OTHER / Number images used: 172000
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Corss correllation coefficient
Output model

PDB-9byb:
Cryo-EM structure of a membrane transport protein

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