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- EMDB-38478: Potassium transporter KtrAB from Bacillus subtilis in ATP-bound s... -

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Basic information

Entry
Database: EMDB / ID: EMD-38478
TitlePotassium transporter KtrAB from Bacillus subtilis in ATP-bound state with addition of EDTA and EGTA, C1 symmetry
Map data
Sample
  • Complex: Bacillus subtilis KtrAB potassium transporter KtrAB
    • Complex: KtrA octamer
      • Protein or peptide: Ktr system potassium uptake protein A
    • Complex: KtrB dimer
      • Protein or peptide: Ktr system potassium uptake protein B
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: SODIUM IONSodium
  • Ligand: POTASSIUM IONPotassium
KeywordsKtrAB / RCK / potassium / transporter / TRANSPORT PROTEIN
Function / homology
Function and homology information


potassium:chloride symporter activity / monoatomic cation transmembrane transporter activity / potassium ion transport / identical protein binding / plasma membrane
Similarity search - Function
TrkH potassium transport family / Cation transporter / Cation transport protein / Regulator of K+ conductance, N-terminal / TrkA-N domain / RCK N-terminal domain profile. / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Ktr system potassium uptake protein A / Ktr system potassium uptake protein B
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsChang YK / Chiang WT / Hu NJ / Tsai MD
Funding support Taiwan, 1 items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis and synergism of ATP and Na+ activation in bacterial K+ uptake system KtrAB
Authors: Chiang WT / Chang YK / Hui WH / Chang SW / Liao CY / Chang YC / Chen CJ / Wang WC / Lai CC / Wang CH / Luo SY / Huang YP / Chou SH / Horng TL / Hou MH / Muench SP / Chen RS / Tsai MD / Hu NJ
History
DepositionDec 27, 2023-
Header (metadata) releaseApr 3, 2024-
Map releaseApr 3, 2024-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38478.png

Downloads & links

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Map

FileDownload / File: emd_38478.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.8866615 - 3.4558973
Average (Standard dev.)0.00033567898 (±0.07056828)
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_38478_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: DeepEMhancer sharpening map

Fileemd_38478_additional_1.map
AnnotationDeepEMhancer sharpening map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_38478_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38478_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Bacillus subtilis KtrAB potassium transporter KtrAB

EntireName: Bacillus subtilis KtrAB potassium transporter KtrAB
Components
  • Complex: Bacillus subtilis KtrAB potassium transporter KtrAB
    • Complex: KtrA octamer
      • Protein or peptide: Ktr system potassium uptake protein A
    • Complex: KtrB dimer
      • Protein or peptide: Ktr system potassium uptake protein B
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: SODIUM IONSodium
  • Ligand: POTASSIUM IONPotassium

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Supramolecule #1: Bacillus subtilis KtrAB potassium transporter KtrAB

SupramoleculeName: Bacillus subtilis KtrAB potassium transporter KtrAB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: KtrAB complex(chain A-L). KtrAB complex in solution was composed of one KtrA octamer (chain A-H) and two KtrB dimer (chain I-J and chain K-L). The molecule weight of KtrAB complex (chain A-L) is 0.393 MDa
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 194 KDa

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Supramolecule #2: KtrA octamer

SupramoleculeName: KtrA octamer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Details: KtrA ocatmer (chain A-H) The molecule weight of KtrA octamer (chain A-H) is 0.199 MDa.
Source (natural)Organism: Bacillus subtilis (bacteria)

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Supramolecule #3: KtrB dimer

SupramoleculeName: KtrB dimer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Details: Two KtrB dimers (chain I-J and chain K-L) The molecule weight of each KtrB dimer is 0.097 MDa

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Macromolecule #1: Ktr system potassium uptake protein A

MacromoleculeName: Ktr system potassium uptake protein A / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 24.91676 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGRIKNKQFA VIGLGRFGGS ICKELHRMGH EVLAVDINEE KVNAYASYAT HAVIANATEE NELLSLGIRN FEYVIVAIGA NIQASTLTT LLLKELDIPN IWVKAQNYYH HKVLEKIGAD RIIHPEKDMG VKIAQSLSDE NVLNYIDLSD EYSIVELLAT R KLDSKSII ...String:
MGRIKNKQFA VIGLGRFGGS ICKELHRMGH EVLAVDINEE KVNAYASYAT HAVIANATEE NELLSLGIRN FEYVIVAIGA NIQASTLTT LLLKELDIPN IWVKAQNYYH HKVLEKIGAD RIIHPEKDMG VKIAQSLSDE NVLNYIDLSD EYSIVELLAT R KLDSKSII DLNVRAKYGC TILAIKHHGD ICLSPAPEDI IREQDCLVIM GHKKDIKRFE NEGM

UniProtKB: Ktr system potassium uptake protein A

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Macromolecule #2: Ktr system potassium uptake protein B

MacromoleculeName: Ktr system potassium uptake protein B / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 48.471539 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTLQKDKVIK WVRFTPPQVL AIGFFLTIII GAVLLMLPIS TTKPLSWIDA LFTAASATTV TGLAVVDTGT QFTVFGQTVI MGLIQIGGL GFMTFAVLIV MILGKKIGLK ERMLVQEALN QPTIGGVIGL VKVLFLFSIS IELIAALILS IRLVPQYGWS S GLFASLFH ...String:
MTLQKDKVIK WVRFTPPQVL AIGFFLTIII GAVLLMLPIS TTKPLSWIDA LFTAASATTV TGLAVVDTGT QFTVFGQTVI MGLIQIGGL GFMTFAVLIV MILGKKIGLK ERMLVQEALN QPTIGGVIGL VKVLFLFSIS IELIAALILS IRLVPQYGWS S GLFASLFH AISAFNNAGF SLWPDNLMSY VGDPTVNLVI TFLFITGGIG FTVLFDVMKN RRFKTFSLHT KLMLTGTLML NA IAMLTVF ILEYSNPGTL GHLHIVDKLW ASYFQAVTPR TAGFNSLDFG SMREGTIVFT LLLMFIGAGS ASTASGIKLT TFI VILTSV IAYLRGKKET VIFRRSIKYP IIIKALAVSV TSLFIVFLGI FALTITEQAP FLQIVFETFS AFGTVGLTMG LTPE LTTAG KCIIIVIMFI GRIGPLTFVF SFAKTEQSNI RYPDGEVFTG

UniProtKB: Ktr system potassium uptake protein B

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 8 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

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Macromolecule #4: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 4 / Number of copies: 4
Molecular weightTheoretical: 22.99 Da

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Macromolecule #5: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: K
Molecular weightTheoretical: 39.098 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

Concentration4 mg/mL
BufferpH: 8
Details: 20 mM Tris-HCl pH 8.0, 70 mM NaCl, 30 mM KCl, 0.75 mM 6-cyclohexyl-1-hexyl-beta-D-maltoside, 2 mM EDTA, 1 mM EGTA, 1 mM ATP
GridModel: UltrAuFoil R2/2 / Material: GOLD / Mesh: 200 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / 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: 2.2 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 105000
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 8613 / Average exposure time: 2.0 sec. / Average electron dose: 54.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 527427
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4j7c


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-8xmi:
Potassium transporter KtrAB from Bacillus subtilis in ATP-bound state with addition of EDTA and EGTA, C1 symmetry

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