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- EMDB-16318: Structure of the K/H exchanger KefC -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-16318
TitleStructure of the K/H exchanger KefC
Map data
Sample
  • Complex: Kefc protein dimer
    • Protein or peptide: Glutathione-regulated potassium-efflux system protein KefC
  • Ligand: POTASSIUM IONPotassium
  • Ligand: ADENOSINE MONOPHOSPHATE
  • Ligand: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
Keywordspotassium proton exchanger / KefC / Transporter / CPA / MEMBRANE PROTEIN
Function / homology
Function and homology information


glutathione-regulated potassium exporter activity / response to methylglyoxal / antiporter activity / toxic substance binding / proton transmembrane transport / enzyme binding / plasma membrane
Similarity search - Function
Glutathione-regulated potassium-efflux system protein KefC / K+/H+ exchanger / Potassium uptake protein TrkA / Sodium/solute symporter superfamily / Cation/H+ exchanger / Sodium/hydrogen exchanger family / Regulator of K+ conductance, N-terminal / TrkA-N domain / RCK N-terminal domain profile. / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Glutathione-regulated potassium-efflux system protein KefC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsGulati A / Drew D
Funding supportEuropean Union, Sweden, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-CoG-820187European Union
Swedish Research Council Sweden
CitationJournal: To be published
Title: Structure and mechanism of the K+/H+ exchanger KefC
Authors: Gulati A / Drew D
History
DepositionDec 8, 2022-
Header (metadata) releaseDec 20, 2023-
Map releaseDec 20, 2023-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16318.png

Downloads & links

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Map

FileDownload / File: emd_16318.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1 Å/pix.
x 240 pix.
= 239.22 Å		1 Å/pix.
x 240 pix.
= 239.22 Å		1 Å/pix.
x 240 pix.
= 239.22 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.99675 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.0
Minimum - Maximum-23.000806999999998 - 39.037224000000002
Average (Standard dev.)0.000000000007308 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 239.22 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_16318_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_16318_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 : Kefc protein dimer

EntireName: Kefc protein dimer
Components
  • Complex: Kefc protein dimer
    • Protein or peptide: Glutathione-regulated potassium-efflux system protein KefC
  • Ligand: POTASSIUM IONPotassium
  • Ligand: ADENOSINE MONOPHOSPHATE
  • Ligand: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate

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Supramolecule #1: Kefc protein dimer

SupramoleculeName: Kefc protein dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Glutathione-regulated potassium-efflux system protein KefC

MacromoleculeName: Glutathione-regulated potassium-efflux system protein KefC
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 61.183223 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDSHTLIQAL IYLGSAALIV PIAVRLGLGS VLGYLIAGCI IGPWGLRLVT DAESILHFAE IGVVLMLFII GLELDPQRLW KLRAAVFGG GALQMVICGG LLGLFCMLLG LRWQVAELIG MTLALSSTAI AMQAMNERNL MVTQMGRSAF AVLLFQDIAA I PLVAMIPL ...String:
MDSHTLIQAL IYLGSAALIV PIAVRLGLGS VLGYLIAGCI IGPWGLRLVT DAESILHFAE IGVVLMLFII GLELDPQRLW KLRAAVFGG GALQMVICGG LLGLFCMLLG LRWQVAELIG MTLALSSTAI AMQAMNERNL MVTQMGRSAF AVLLFQDIAA I PLVAMIPL LATSSASTTM GAFALSALKV AGALVLVVLL GRYVTRPALR FVARSGLREV FSAVALFLVF GFGLLLEEVG LS MAMGAFL AGVLLASSEY RHALESDIEP FKGLLLGLFF IGVGMSIDFG TLLENPLRIV ILLLGFLIIK IAMLWLIARP LQV PNKQRR WFAVLLGQGS EFAFVVFGAA QMANVLEPEW AKSLTLAVAL SMAATPILLV ILNRLEQSST EEAREADEID EEQP RVIIA GFGRFGQITG RLLLSSGVKM VVLDHDPDHI ETLRKFGMKV FYGDATRMDL LESAGAAKAE VLINAIDDPQ TNLQL TEMV KEHFPHLQII ARARDVDHYI RLRQAGVEKP ERETFEGALK TGRLALESLG LGPYEARERA DVFRRFNIQM VEEMAM V

UniProtKB: Glutathione-regulated potassium-efflux system protein KefC

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Macromolecule #2: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #3: ADENOSINE MONOPHOSPHATE

MacromoleculeName: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: AMP
Molecular weightTheoretical: 347.221 Da
Chemical component information

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM / Adenosine monophosphate

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Macromolecule #4: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]o...

MacromoleculeName: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
type: ligand / ID: 4 / Number of copies: 2 / Formula: PGW
Molecular weightTheoretical: 749.007 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

BufferpH: 7.5
GridMaterial: COPPER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 52.2 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 305737
FSC plot (resolution estimation)

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