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Open data
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Basic information
Entry | Database: PDB / ID: 7lc3 | ||||||||||||
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Title | CryoEM Structure of KdpFABC in E1-ATP state | ||||||||||||
![]() | (Potassium-transporting ATPase ...) x 4 | ||||||||||||
![]() | MEMBRANE PROTEIN / P-type ATPase / ATP-dependent potassium pump | ||||||||||||
Function / homology | ![]() P-type K+ transporter / P-type potassium transmembrane transporter activity / potassium:proton antiporter complex / potassium ion-transporting ATPase complex / monoatomic cation transmembrane transport / potassium ion binding / potassium ion transmembrane transport / potassium ion transport / magnesium ion binding / ATP hydrolysis activity ...P-type K+ transporter / P-type potassium transmembrane transporter activity / potassium:proton antiporter complex / potassium ion-transporting ATPase complex / monoatomic cation transmembrane transport / potassium ion binding / potassium ion transmembrane transport / potassium ion transport / magnesium ion binding / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.23 Å | ||||||||||||
![]() | Sweet, M.E. / Larsen, C. / Pedersen, B.P. / Stokes, D.L. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Structural basis for potassium transport in prokaryotes by KdpFABC. Authors: Marie E Sweet / Casper Larsen / Xihui Zhang / Michael Schlame / Bjørn P Pedersen / David L Stokes / ![]() ![]() Abstract: KdpFABC is an oligomeric K transport complex in prokaryotes that maintains ionic homeostasis under stress conditions. The complex comprises a channel-like subunit (KdpA) from the superfamily of K ...KdpFABC is an oligomeric K transport complex in prokaryotes that maintains ionic homeostasis under stress conditions. The complex comprises a channel-like subunit (KdpA) from the superfamily of K transporters and a pump-like subunit (KdpB) from the superfamily of P-type ATPases. Recent structural work has defined the architecture and generated contradictory hypotheses for the transport mechanism. Here, we use substrate analogs to stabilize four key intermediates in the reaction cycle and determine the corresponding structures by cryogenic electron microscopy. We find that KdpB undergoes conformational changes consistent with other representatives from the P-type superfamily, whereas KdpA, KdpC, and KdpF remain static. We observe a series of spherical densities that we assign as K or water and which define a pathway for K transport. This pathway runs through an intramembrane tunnel in KdpA and delivers ions to sites in the membrane domain of KdpB. Our structures suggest a mechanism where ATP hydrolysis is coupled to K transfer between alternative sites in KdpB, ultimately reaching a low-affinity site where a water-filled pathway allows release of K to the cytoplasm. | ||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 466.7 KB | Display | ![]() |
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PDB format | ![]() | 381.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 23268MC ![]() 7bgyC ![]() 7bh1C ![]() 7bh2C ![]() 7lc6C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Potassium-transporting ATPase ... , 4 types, 4 molecules ABCD
#1: Protein | Mass: 59247.684 Da / Num. of mol.: 1 / Mutation: Q116R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: kdpA, b0698, JW0686 / Plasmid: pSD107 / Production host: ![]() ![]() |
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#2: Protein | Mass: 72251.867 Da / Num. of mol.: 1 / Mutation: S162A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: kdpB, b0697, JW0685 / Plasmid: pSD107 / Production host: ![]() ![]() |
#3: Protein | Mass: 22299.225 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: kdpC, b0696, JW0684 / Plasmid: pSD107 / Production host: ![]() ![]() |
#4: Protein/peptide | Mass: 3071.714 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: kdpF, b4513, JW0687 / Plasmid: pSD107 / Production host: ![]() ![]() |
-Non-polymers , 5 types, 15 molecules ![](data/chem/img/K.gif)
![](data/chem/img/9Y0.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ACP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/9Y0.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ACP.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Chemical | ChemComp-9Y0 / ( | #7: Chemical | ChemComp-MG / | #8: Chemical | ChemComp-ACP / | #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: KdpFABC in E1-ATP state / Type: COMPLEX Details: KdpFABC complex solublized in decyl maltopyranoside (DM) detergent. Entity ID: #1-#4 / Source: RECOMBINANT | ||||||||||||||||||||||||||||||||||||||||
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Molecular weight | Value: 0.16 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||||||||||||
Source (natural) | Organism: ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 Details: AMPPCP was added to the protein after size-exclusion chromatography and incubated 1 hr prior to freezing | ||||||||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 4.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: DM-solublized KdpFABC complex purified through SEC the same day as grid freezing. Peak fraction diluted to 4.5 mg/mL and complexed with AMP-PCP solution prior to application to grid. | ||||||||||||||||||||||||||||||||||||||||
Specimen support | Details: PELCO easiGlow Glow Discharge Cleaning System used for glow discharge with default settings. Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3 | ||||||||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 77 K / Temperature (min): 77 K |
Image recording | Average exposure time: 10 sec. / Electron dose: 75 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2394 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
Image scans | Sampling size: 5 µm / Width: 3710 / Height: 3838 / Movie frames/image: 50 / Used frames/image: 1-50 |
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Processing
Software | Name: PHENIX / Version: dev_3758: / Classification: refinement | ||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 552005 / Details: template picking | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 245466 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation coefficient | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5MRW Accession code: 5MRW / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||
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