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- EMDB-19816: Structure of KefC Asp156Asn variant -

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Basic information

Entry
Database: EMDB / ID: EMD-19816
TitleStructure of KefC Asp156Asn variant
Map data
Sample
  • Complex: Homodimer of KefC Asp156Asn variant
    • Protein or peptide: Glutathione-regulated potassium-efflux system protein KefC
  • Ligand: ADENOSINE MONOPHOSPHATE
  • Ligand: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
KeywordsKefC / Potassium / GSH / Mutant / TRANSPORT PROTEIN
Function / homology
Function and homology information


glutathione-regulated potassium exporter activity / response to methylglyoxal / potassium:proton antiporter complex / intracellular pH elevation / regulation of pH / antiporter activity / toxic substance binding / proton transmembrane transport / regulation of intracellular pH / potassium ion transport ...glutathione-regulated potassium exporter activity / response to methylglyoxal / potassium:proton antiporter complex / intracellular pH elevation / regulation of pH / antiporter activity / toxic substance binding / proton transmembrane transport / regulation of intracellular pH / potassium ion transport / response to hydrogen peroxide / response to toxic substance / nucleotide binding / enzyme binding / protein homodimerization activity / membrane / 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: 2.98 Å
AuthorsGulati A / Kokane S / Drew D
Funding support Sweden, European Union, 2 items
OrganizationGrant numberCountry
Swedish Research Council Sweden
European Research Council (ERC)European Union
CitationJournal: To Be Published
Title: Structure of KefC Asp156Asn variant
Authors: Gulati A / Kokane S / Drew D
History
DepositionMar 7, 2024-
Header (metadata) releaseJun 5, 2024-
Map releaseJun 5, 2024-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19816.png

Downloads & links

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Map

FileDownload / File: emd_19816.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.9967 Å
Density
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.23022266 - 0.5673169
Average (Standard dev.)0.0010446795 (±0.01653188)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 239.208 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19816_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map

Fileemd_19816_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_19816_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_19816_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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Sample components

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Entire : Homodimer of KefC Asp156Asn variant

EntireName: Homodimer of KefC Asp156Asn variant
Components
  • Complex: Homodimer of KefC Asp156Asn variant
    • Protein or peptide: Glutathione-regulated potassium-efflux system protein KefC
  • 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: Homodimer of KefC Asp156Asn variant

SupramoleculeName: Homodimer of KefC Asp156Asn variant / 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: 61.182238 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDSHTLIQAL IYLGSAALIV PIAVRLGLGS VLGYLIAGCI IGPWGLRLVT DAESILHFAE IGVVLMLFII GLELDPQRLW KLRAAVFGG GALQMVICGG LLGLFCMLLG LRWQVAELIG MTLALSSTAI AMQAMNERNL MVTQMGRSAF AVLLFQNIAA I PLVAMIPL ...String:
MDSHTLIQAL IYLGSAALIV PIAVRLGLGS VLGYLIAGCI IGPWGLRLVT DAESILHFAE IGVVLMLFII GLELDPQRLW KLRAAVFGG GALQMVICGG LLGLFCMLLG LRWQVAELIG MTLALSSTAI AMQAMNERNL MVTQMGRSAF AVLLFQNIAA 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: ADENOSINE MONOPHOSPHATE

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

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM

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Macromolecule #3: (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: 3 / 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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 327001
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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