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- EMDB-14917: Cryo-EM map of the WT KdpFABC complex in the E1-P_ADP conformatio... -
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Basic information
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Title | Cryo-EM map of the WT KdpFABC complex in the E1-P_ADP conformation, under turnover conditions | ||||||||||||||||||
![]() | Cryo-EM map of the WT KdpFABC complex, in the E1-P_ADP conformation, at 3.1 A resolution, sharpened at -122 A2. Data obtained in the presence under turnover conditions | ||||||||||||||||||
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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 | single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||||||||
![]() | Hielkema L / Stock C / Silberberg JM / Corey RA / Wunnicke D / Dubach VRA / Stansfeld PJ / Haenelt I / Paulino C | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Inhibited KdpFABC transitions into an E1 off-cycle state. Authors: Jakob M Silberberg / Charlott Stock / Lisa Hielkema / Robin A Corey / Jan Rheinberger / Dorith Wunnicke / Victor R A Dubach / Phillip J Stansfeld / Inga Hänelt / Cristina Paulino / ![]() ![]() ![]() Abstract: KdpFABC is a high-affinity prokaryotic K uptake system that forms a functional chimera between a channel-like subunit (KdpA) and a P-type ATPase (KdpB). At high K levels, KdpFABC needs to be ...KdpFABC is a high-affinity prokaryotic K uptake system that forms a functional chimera between a channel-like subunit (KdpA) and a P-type ATPase (KdpB). At high K levels, KdpFABC needs to be inhibited to prevent excessive K accumulation to the point of toxicity. This is achieved by a phosphorylation of the serine residue in the TGES motif in the A domain of the pump subunit KdpB (KdpB). Here, we explore the structural basis of inhibition by KdpB phosphorylation by determining the conformational landscape of KdpFABC under inhibiting and non-inhibiting conditions. Under turnover conditions, we identified a new inhibited KdpFABC state that we termed E1P tight, which is not part of the canonical Post-Albers transport cycle of P-type ATPases. It likely represents the biochemically described stalled E1P state adopted by KdpFABC upon KdpB phosphorylation. The E1P tight state exhibits a compact fold of the three cytoplasmic domains and is likely adopted when the transition from high-energy E1P states to E2P states is unsuccessful. This study represents a structural characterization of a biologically relevant off-cycle state in the P-type ATPase family and supports the emerging discussion of P-type ATPase regulation by such states. | ||||||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 49.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 25.9 KB 25.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.6 KB | Display | ![]() |
Images | ![]() | 28.2 KB | ||
Masks | ![]() | 52.7 MB | ![]() | |
Others | ![]() ![]() | 40.8 MB 40.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7zrkMC ![]() 7zrdC ![]() 7zreC ![]() 7zrgC ![]() 7zrhC ![]() 7zriC ![]() 7zrjC ![]() 7zrlC ![]() 7zrmC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Cryo-EM map of the WT KdpFABC complex, in the E1-P_ADP conformation, at 3.1 A resolution, sharpened at -122 A2. Data obtained in the presence under turnover conditions | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.012 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: Half map 1 used during refinement and for...
File | emd_14917_half_map_1.map | ||||||||||||
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Annotation | Half map 1 used during refinement and for FSC gold-standard resolution calculation of the WT KdpFABC complex in the E1-P_ADP conformation under turnover conditions | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2 used during refinement and for...
File | emd_14917_half_map_2.map | ||||||||||||
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Annotation | Half map 2 used during refinement and for FSC gold-standard resolution calculation of the WT KdpFABC complex in the E1-P_ADP conformation under turnover conditions | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : KdpFABC
Entire | Name: KdpFABC |
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Components |
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-Supramolecule #1: KdpFABC
Supramolecule | Name: KdpFABC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
Molecular weight | Theoretical: 157 KDa |
-Macromolecule #1: Potassium-transporting ATPase potassium-binding subunit
Macromolecule | Name: Potassium-transporting ATPase potassium-binding subunit type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 59.218613 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MAAQGFLLIA TFLLVLMVLA RPLGSGLARL INDIPLPGTT GVERVLFRAL GVSDREMNWK QYLCAILGLN MLGLAVLFFM LLGQHYLPL NPQQLPGLSW DLALNTAVSF VTNTNWQSYS GETTLSYFSQ MAGLTVQNFL SAASGIAVIF ALIRAFTRQS M STLGNAWV ...String: MAAQGFLLIA TFLLVLMVLA RPLGSGLARL INDIPLPGTT GVERVLFRAL GVSDREMNWK QYLCAILGLN MLGLAVLFFM LLGQHYLPL NPQQLPGLSW DLALNTAVSF VTNTNWQSYS GETTLSYFSQ MAGLTVQNFL SAASGIAVIF ALIRAFTRQS M STLGNAWV DLLRITLWVL VPVALLIALF FIQQGALQNF LPYQAVNTVE GAQQLLPMGP VASQEAIKML GTNGGGFFNA NS SHPFENP TALTNFVQML AIFLIPTALC FAFGEVMGDR RQGRMLLWAM SVIFVICVGV VMWAEVQGNP HLLALGTDSS INM EGKESR FGVLVSSLFA VVTTAASCGA VIAMHDSFTA LGGMVPMWLM QIGEVVFGGV GSGLYGMMLF VLLAVFIAGL MIGR TPEYL GKKIDVREMK LTALAILVTP TLVLMGAALA MMTDAGRSAM LNPGPHGFSE VLYAVSSAAN NNGSAFAGLS ANSPF WNCL LAFCMFVGRF GVIIPVMAIA GSLVSKKSQA ASSGTLPTHG PLFVGLLIGT VLLVGALTFI PALALGPVAE YLS |
-Macromolecule #2: Potassium-transporting ATPase KdpC subunit
Macromolecule | Name: Potassium-transporting ATPase KdpC subunit / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 20.281035 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSGLRPALST FIFLLLITGG VYPLLTTVLG QWWFPWQANG SLIREGDTVR GSALIGQNFT GNGYFHGRPS ATAEMPYNPQ ASGGSNLAV SNPELDKLIA ARVAALRAAN PDASASVPVE LVTASASGLD NNITPQAAAW QIPRVAKARN LSVEQLTQLI A KYSQQPLV KYIGQPVVNI VELNLALDKL DE |
-Macromolecule #3: Potassium-transporting ATPase KdpF subunit
Macromolecule | Name: Potassium-transporting ATPase KdpF subunit / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 2.853463 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSAGVITGVL LVFLLLGYLV YALINAE |
-Macromolecule #4: Potassium-transporting ATPase ATP-binding subunit
Macromolecule | Name: Potassium-transporting ATPase ATP-binding subunit / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: P-type K+ transporter |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 72.42782 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSRKQLALFE PTLVVQALKE AVKKLNPQAQ WRNPVMFIVW IGSLLTTCIS IAMASGAMPG NALFSAAISG WLWITVLFAN FAEALAEGR SKAQANSLKG VKKTAFARKL REPKYGAAAD KVPADQLRKG DIVLVEAGDI IPCDGEVIEG GASVDESAIT G E(SEP)APVIRE ...String: MSRKQLALFE PTLVVQALKE AVKKLNPQAQ WRNPVMFIVW IGSLLTTCIS IAMASGAMPG NALFSAAISG WLWITVLFAN FAEALAEGR SKAQANSLKG VKKTAFARKL REPKYGAAAD KVPADQLRKG DIVLVEAGDI IPCDGEVIEG GASVDESAIT G E(SEP)APVIRE SGGDFASVTG GTRILSDWLV IECSVNPGET FLDRMIAMVE GAQRRKTPNE IALTILLIAL TIVFLLAT A TLWPFSAWGG NAVSVTVLVA LLVCLIPTTI GGLLSAIGVA GMSRMLGANV IATSGRAVEA AGDVDVLLL(PHD) KTGTI TLGN RQASEFIPAQ GVDEKTLADA AQLASLADET PEGRSIVILA KQRFNLRERD VQSLHATFVP FTAQSRMSGI NIDNRM IRK GSVDAIRRHV EANGGHFPTD VDQKVDQVAR QGATPLVVVE GSRVLGVIAL KDIVKGGIKE RFAQLRKMGI KTVMITG DN RLTAAAIAAE AGVDDFLAEA TPEAKLALIR QYQAEGRLVA MTGDGTNDAP ALAQADVAVA MNSGTQAAKE AGNMVDLD S NPTKLIEVVH IGKQMLMTRG SLTTFSIAND VAKYFAIIPA AFAATYPQLN ALNIMCLHSP DSAILSAVIF NALIIVFLI PLALKGVSYK PLTASAMLRR NLWIYGLGGL LVPFIGIKVI DLLLTVCGLV |
-Macromolecule #5: POTASSIUM ION
Macromolecule | Name: POTASSIUM ION / type: ligand / ID: 5 / Number of copies: 12 / Formula: K |
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Molecular weight | Theoretical: 39.098 Da |
-Macromolecule #6: CARDIOLIPIN
Macromolecule | Name: CARDIOLIPIN / type: ligand / ID: 6 / Number of copies: 2 / Formula: CDL |
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Molecular weight | Theoretical: 1.464043 KDa |
Chemical component information | ![]() ChemComp-CDL: |
-Macromolecule #7: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 1 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ![]() ChemComp-ADP: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 8 Details: 10 mM Tris-HCl pH 8, 10 mM MgCl2, 10 mM NaCl and 0.0125% DDM |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Details: at 5 mA |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Temperature | Min: 90.0 K / Max: 105.0 K |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-60 / Number grids imaged: 3 / Number real images: 17938 / Average exposure time: 9.0 sec. / Average electron dose: 52.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.0 µm / Calibrated defocus min: 0.5 µm / Calibrated magnification: 49407 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 49407 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |