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- EMDB-42798: Magnesium transporter MgtA dimer from E. coli in 5 mM MgCl2 and 5... -

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Basic information

Entry
Database: EMDB / ID: EMD-42798
TitleMagnesium transporter MgtA dimer from E. coli in 5 mM MgCl2 and 5 mM ATPyS
Map data
Sample
  • Complex: Magnesium transporter MgtA from Escherichia coli in the dimeric form in the presence of 5 mM MgCl2 and 5 mM ATPyS
    • Protein or peptide: Magnesium-transporting ATPase, P-type 1
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
Keywordsmagnesium / transport / membrane protein / 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
Magnesium-transporting ATPase, P-type 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.87 Å
AuthorsZeinert R / Zhou F / Cavalcanti Franco PH / Zoeller J / Lessen H / Iyer A / Langer JD / Sodt AJ / Storz G / Matthies D
Funding support United States, Germany, 6 items
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: To Be Published
Title: Magnesium Transporter MgtA revealed as a Dimeric P-type ATPase
Authors: Zeinert R / Zhou F / Cavalcanti Franco PH / Zoeller J / Lessen H / Iyer A / Langer JD / Sodt AJ / Storz G / Matthies D
History
DepositionNov 13, 2023-
Header (metadata) releaseNov 27, 2024-
Map releaseNov 27, 2024-
UpdateNov 27, 2024-
Current statusNov 27, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42798.png

Downloads & links

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Map

FileDownload / File: emd_42798.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.)
0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å

Surface

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Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.333
Minimum - Maximum-0.4169342 - 1.0702271
Average (Standard dev.)0.005012141 (±0.033214234)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 318.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_42798_msk_1.map
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Additional map: #2

Fileemd_42798_additional_1.map
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Additional map: #1

Fileemd_42798_additional_2.map
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Half map: #2

Fileemd_42798_half_map_1.map
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Half map: #1

Fileemd_42798_half_map_2.map
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Sample components

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Entire : Magnesium transporter MgtA from Escherichia coli in the dimeric f...

EntireName: Magnesium transporter MgtA from Escherichia coli in the dimeric form in the presence of 5 mM MgCl2 and 5 mM ATPyS
Components
  • Complex: Magnesium transporter MgtA from Escherichia coli in the dimeric form in the presence of 5 mM MgCl2 and 5 mM ATPyS
    • Protein or peptide: Magnesium-transporting ATPase, P-type 1
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

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Supramolecule #1: Magnesium transporter MgtA from Escherichia coli in the dimeric f...

SupramoleculeName: Magnesium transporter MgtA from Escherichia coli in the dimeric form in the presence of 5 mM MgCl2 and 5 mM ATPyS
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli) / Strain: Escherichia coli K-12
Molecular weightTheoretical: 201 KDa

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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
Source (natural)Organism: Escherichia coli (E. coli) / Strain: Escherichia coli K-12
Molecular weightTheoretical: 100.393062 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MFKEIFTRLI RHLPSRLVHR DPLPGAQQTV NTVVPPSLSA HCLKMAVMPE EELWKTFDTH PEGLNQAEVE SAREQHGENK LPAQQPSPW WVHLWVCYRN PFNILLTILG AISYATEDLF AAGVIALMVA ISTLLNFIQE ARSTKAADAL KAMVSNTATV L RVINDKGE ...String:
MFKEIFTRLI RHLPSRLVHR DPLPGAQQTV NTVVPPSLSA HCLKMAVMPE EELWKTFDTH PEGLNQAEVE SAREQHGENK LPAQQPSPW WVHLWVCYRN PFNILLTILG AISYATEDLF AAGVIALMVA ISTLLNFIQE ARSTKAADAL KAMVSNTATV L RVINDKGE NGWLEIPIDQ LVPGDIIKLA AGDMIPADLR ILQARDLFVA QASLTGESLP VEKAATTRQP EHSNPLECDT LC FMGTTVV SGTAQAMVIA TGANTWFGQL AGRVSEQESE PNAFQQGISR VSMLLIRFML VMAPVVLLIN GYTKGDWWEA ALF ALSVAV GLTPEMLPMI VTSTLARGAV KLSKQKVIVK HLDAIQNFGA MDILCTDKTG TLTQDKIVLE NHTDISGKTS ERVL HSAWL NSHYQTGLKN LLDTAVLEGT DEESARSLAS RWQKIDEIPF DFERRRMSVV VAENTEHHQL VCKGALQEIL NVCSQ VRHN GEIVPLDDIM LRKIKRVTDT LNRQGLRVVA VATKYLPARE GDYQRADESD LILEGYIAFL DPPKETTAPA LKALKA SGI TVKILTGDSE LVAAKVCHEV GLDAGEVVIG SDIETLSDDE LANLAQRTTL FARLTPMHKE RIVTLLKREG HVVGFMG DG INDAPALRAA DIGISVDGAV DIAREAADII LLEKSLMVLE EGVIEGRRTF ANMLKYIKMT ASSNFGNVFS VLVASAFL P FLPMLPLHLL IQNLLYDVSQ VAIPFDNVDD EQIQKPQRWN PADLGRFMIF FGPISSIFDI LTFCLMWWVF HANTPETQT LFQSGWFVVG LLSQTLIVHM IRTRRVPFIQ SCASWPLMIM TVIVMIVGIA LPFSPLASYL QLQALPLSYF PWLVAILAGY MTLTQLVKG FYSRRYGWQH HHHHH

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: 6 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #3: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 2 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*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

Concentration2.3 mg/mL
BufferpH: 7.5
Details: 50 mM Tris/HCl, 50 mM K2SO4, 5 mM MgCl2, 0.007% glycol-diosgenin, 2 mM DTT, 5 mM ATPyS
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 88 % / Chamber temperature: 278 K / Instrument: LEICA EM GP
DetailsE. coli MgtA purified with a C-terminal His-tag

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 9868 / Average exposure time: 3.795 sec. / Average electron dose: 50.0 e/Å2
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.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated magnification: 60241 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber 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).
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 28120
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: experimental model / Details: our new MgtA dimer structure without nucleotides
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8uyb:
Magnesium transporter MgtA dimer from E. coli in 5 mM MgCl2 and 5 mM ATPyS

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Atomic model buiding 2

Initial modelChain - Source name: Other / Chain - Initial model type: experimental model / Details: our new MgtA dimer structure without nucleotides
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8uyb:
Magnesium transporter MgtA dimer from E. coli in 5 mM MgCl2 and 5 mM ATPyS

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Atomic model buiding 3

Initial modelChain - Source name: Other / Chain - Initial model type: experimental model / Details: our new MgtA dimer structure without nucleotides
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8uyb:
Magnesium transporter MgtA dimer from E. coli in 5 mM MgCl2 and 5 mM ATPyS

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