[English] 日本語
Yorodumi
- EMDB-74405: Cryo-EM structure of MgtA with bound AMPPCP and magnesium -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-74405
TitleCryo-EM structure of MgtA with bound AMPPCP and magnesium
Map data
Sample
  • Organelle or cellular component: Magnesium-transporting P-type ATPase A
    • Protein or peptide: Magnesium-transporting ATPase, P-type 1
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: POTASSIUM ION
  • Ligand: water
KeywordsP-type ATPase / membrane Transport / TRANSPORT PROTEIN / MgtA / AMPPCP
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) / Lactococcus cremoris (lactic acid bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.79 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
DepositionDec 8, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_74405.png

Downloads & links

-
Map

FileDownload / File: emd_74405.map.gz / Format: CCP4 / Size: 216 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 384 pix.
= 357.12 Å		0.93 Å/pix.
x 384 pix.
= 357.12 Å		0.93 Å/pix.
x 384 pix.
= 357.12 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: 0.111
Minimum - Maximum-0.45989805 - 0.9387377
Average (Standard dev.)0.0001966161 (±0.013020023)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 357.12 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_74405_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_74405_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Magnesium-transporting P-type ATPase A

EntireName: Magnesium-transporting P-type ATPase A
Components
  • Organelle or cellular component: Magnesium-transporting P-type ATPase A
    • Protein or peptide: Magnesium-transporting ATPase, P-type 1
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: POTASSIUM ION
  • Ligand: water

-
Supramolecule #1: Magnesium-transporting P-type ATPase A

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

-
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 cremoris (lactic acid bacteria)
Molecular weightTheoretical: 102.114453 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHHHL EMKKLRKTLE NTKRATNFVD NNEIKRRLEF ARVSSKEELF QKFKTSDKGL SEEQVEISRE QYGDNSITRG KKTSLIKRL YQAFINPFTI ILFVLALVSA FTDIILAAPG EKNPQGLIII TTMVLISGIL RFVQETRSGN AAENLLKMIT T TTNVHRLE ...String:
MHHHHHHHHL EMKKLRKTLE NTKRATNFVD NNEIKRRLEF ARVSSKEELF QKFKTSDKGL SEEQVEISRE QYGDNSITRG KKTSLIKRL YQAFINPFTI ILFVLALVSA FTDIILAAPG EKNPQGLIII TTMVLISGIL RFVQETRSGN AAENLLKMIT T TTNVHRLE TGSQEIPIEE VLVGDIIHLS AGDMVPADLR IIQAKDLFIS QASLTGESEP VEKLDLATSE AYDSITESSN LA FMGSNII SGSAYGIVIV TGDTTIFGEM ARSVTEDSTK TTFEKGVNSF SWVLIRFMLV MVPFVLLING FTKGDWMEAA LFA LAVAVG LTPAMLPMIV TTCLAKGAVT MSKEKTIIKN LNSIQNLGSM NILCTDKTGT LTQDKVVLMR HLDIHGQENI RVLR HGFLN SYYQTGLKNL MDLAIIEGAE AKQEKNPELS GLSSKYTKVD EIPFDFERRR MSVVVQSNGN GTDSKTQMIT KGAAE EMLD ICTLVEDEGK IVPLNSELRQ YILKKVDKLN ELGMRVILVA QKTNPSPIDS FSVQDESEMV LMGYLAFLDP PKESTA KAI KALNKYGVSV KILTGDNDKV TRSVCEQVGL PADKTILGSD IDQLDDEELA QVAKEASVFA KLSPQQKARI VTTLRNS GN SVGYMGDGIN DAAAMKASDV GISVDSAVDI AKESADVILL EKDLMVLEKG IIEGRKTYAN MIKYIKMTAS SNFGNMFS V LIASAFLPFI PMLSIHILLL NLIYDFSCTA IPWDNVDEEY LVVPRKWDAS SVSKFMLWIG PTSSVFDITT YLLMFFVIC PATFGPFSTL VPGSAAYIGF IALFHTGWFV ESMWTQTLVI HMIRTPKIPF LQSRASAPLT LLTFLGIIGL TIIPFTSFGK SIGLMALPL TFFPWLILTV VMYMFLVTLF KKIFVSKYGE LL

UniProtKB: Magnesium-transporting ATPase, P-type 1

-
Macromolecule #2: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER

MacromoleculeName: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / type: ligand / ID: 2 / Number of copies: 1 / Formula: ACP
Molecular weightTheoretical: 505.208 Da
Chemical component information

ChemComp-ACP:
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / AMP-PCP, energy-carrying molecule analogue*YM

-
Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #4: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: K
Molecular weightTheoretical: 39.098 Da

-
Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 26 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 577882
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more