[English] 日本語
Yorodumi
- PDB-8uyb: Magnesium transporter MgtA dimer from E. coli in 5 mM MgCl2 and 5... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8uyb
TitleMagnesium transporter MgtA dimer from E. coli in 5 mM MgCl2 and 5 mM ATPyS
ComponentsMagnesium-transporting ATPase, P-type 1
KeywordsMEMBRANE PROTEIN / magnesium / transport / dimer / oligomer / cryo-EM / P-type ATPase / ion translocation
Function / homology
Function and homology information


P-type Mg2+ transporter / P-type magnesium transporter activity / magnesium ion transmembrane transport / P-type ion transporter activity / cellular response to magnesium ion / ATPase-coupled monoatomic cation transmembrane transporter activity / intracellular membrane-bounded organelle / ATP hydrolysis activity / ATP binding / metal ion 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 / E1-E2 ATPase / 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 / E1-E2 ATPase / 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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Magnesium-transporting ATPase, P-type 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.87 Å
AuthorsZeinert, R. / Zhou, F. / Cavalcanti Franco, P.H. / Zoeller, J. / Lessen, H. / Iyer, A. / Langer, J.D. / Sodt, A.J. / Storz, G. / Matthies, D.
Funding support United States, Germany, 6items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)ZIA HD008998 United States
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)ZIA HD008855 United States
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)ZIA HD008955 United States
National Institutes of Health/National Library of Medicine (NIH/NLM)LM594244 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1FI2GM146628-01 United States
German Research Foundation (DFG)3542/1-1 Germany
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: P-type ATPase magnesium transporter MgtA acts as a dimer.
Authors: Rilee Zeinert / Fei Zhou / Pedro Franco / Jonathan Zöller / Zaid K Madni / Henry Lessen / L Aravind / Julian D Langer / Alexander J Sodt / Gisela Storz / Doreen Matthies /
Abstract: Magnesium (Mg) uptake systems are present in all domains of life, consistent with the vital role of this ion. P-type ATPase Mg importers are required for bacterial growth when Mg is limiting or ...Magnesium (Mg) uptake systems are present in all domains of life, consistent with the vital role of this ion. P-type ATPase Mg importers are required for bacterial growth when Mg is limiting or during pathogenesis. However, insights into their mechanisms of action are missing. Here we solved the cryo-EM structure of the Mg transporter MgtA from Escherichia coli. We obtained high-resolution structures of both homodimeric (2.9 Å) and monomeric (3.6 Å) forms. The dimer structure is formed by multiple contacts between residues in adjacent soluble N and P subdomains. Our structures revealed an ion, assigned as Mg, in the transmembrane segment. Moreover, we detected two cytoplasmic ion-binding sites and determined the structure of the N-terminal tail. Sequence conservation, mutagenesis and ATPase assays indicate dimerization, the ion-binding sites and the N-terminal tail facilitate cation transport or serve regulatory roles.
History
DepositionNov 13, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Magnesium-transporting ATPase, P-type 1
B: Magnesium-transporting ATPase, P-type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,97810
Polymers200,7862
Non-polymers1,1928
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein Magnesium-transporting ATPase, P-type 1


Mass: 100393.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: Escherichia coli K-12 / Gene: mgtA / Plasmid: pETDuet-1
Details (production host): pETDuet-1 is designed for the coexpression of two target genes. pETDuet-1 carries the pBR322-derived ColE1 replicon, the lacI gene and the ampicillin resistance gene.
Production host: Escherichia coli (E. coli) / Strain (production host): Escherichia coli C43 (DE3) / References: UniProt: P0ABB8
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Magnesium transporter MgtA from Escherichia coli in the dimeric form in the presence of 5 mM MgCl2 and 5 mM ATPyS
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.201 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: Escherichia coli K-12
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: Escherichia coli C43 (DE3) / Plasmid: pETDuet-1
Buffer solutionpH: 7.5
Details: 50 mM Tris/HCl, 50 mM K2SO4, 5 mM MgCl2, 0.007% glycol-diosgenin, 2 mM DTT, 5 mM ATPyS
SpecimenConc.: 2.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: E. coli MgtA purified with a C-terminal His-tag
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 88 % / Chamber temperature: 278 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Calibrated magnification: 60241 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3.795 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 9868
Details: A first dataset was collected with a dose rate of 9 A/px/s (~7.5 on the camera through the sample), exposure time 0.076 s/frame (~1 e-/A2) and total exposure time of 3.795 s per movie (~50 e- ...Details: A first dataset was collected with a dose rate of 9 A/px/s (~7.5 on the camera through the sample), exposure time 0.076 s/frame (~1 e-/A2) and total exposure time of 3.795 s per movie (~50 e-/A2), resulting in a total of 3396 movies with 50 frames each. A second dataset was collected with a dose rate of 9 A/px/s (~7.5 on the camera through the sample), exposure time 0.076 s/frame (~1 e-/A2) and total exposure time of 3.795 s per movie (~50 e-/A2), resulting in a total of 6472 movies with 50 frames each.
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

-
Processing

EM software
IDNameVersionCategoryFitting-ID
1cisTEMparticle selection
3SerialEM3.8-11image acquisition
5cisTEMCTF correction
8UCSF Chimera8.6.10model fitting1
11cryoSPARCCTF correction
13Coot0.9.8.7model fitting2
14Coot0.9.8.7model refinement2
15PHENIX1.20.1-4487model fitting3
16PHENIX1.20.1-4487model refinement3
17cryoSPARCinitial Euler assignment
19cryoSPARCfinal Euler assignment
21cryoSPARCclassification
23cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1783325
Details: 454,311 particles were initially selected from dataset 1 (2,849 selected movies from 3,396 total). 1,329,014 particles were initially selected from dataset 2 (6,337 selected movies from 6,472 total).
3D reconstructionResolution: 3.87 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 28120 / Symmetry type: POINT
Atomic model building
IDProtocolSpace
1RIGID BODY FITREAL
2FLEXIBLE FITREAL
3FLEXIBLE FITREAL
Atomic model building
ID 3D fitting-IDDetailsSource nameType
11our new MgtA dimer structure without nucleotidesOtherexperimental model
22our new MgtA dimer structure without nucleotidesOtherexperimental model
33our new MgtA dimer structure without nucleotidesOtherexperimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00214168
ELECTRON MICROSCOPYf_angle_d0.55819312
ELECTRON MICROSCOPYf_dihedral_angle_d5.851926
ELECTRON MICROSCOPYf_chiral_restr0.042284
ELECTRON MICROSCOPYf_plane_restr0.0052452

+
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