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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-12482 | ||||||||||||||||||
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Title | Rb-loaded cryo-EM structure of the E1-ATP KdpFABC complex. | ||||||||||||||||||
![]() | Rb-loaded E1-ATP map of the KdpFABC complex at 3.2 A resolution sharpened at -130 A2. Data obtained in the presence of 100 mM RbCl, 1 mM ATP, 10 mM AMPPCP. | ||||||||||||||||||
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![]() | P-type ATPase / superfamily of K+ transporters (SKT) / Rb substitution / intersubunit tunnel / MEMBRANE PROTEIN | ||||||||||||||||||
Function / homology | ![]() P-type K+ transporter / P-type potassium transmembrane transporter activity / potassium:proton antiporter complex / potassium ion-transporting ATPase complex / plasma membrane => GO:0005886 / monoatomic cation transmembrane transport / potassium ion binding / potassium ion transmembrane transport / potassium ion transport / hydrolase activity ...P-type K+ transporter / P-type potassium transmembrane transporter activity / potassium:proton antiporter complex / potassium ion-transporting ATPase complex / plasma membrane => GO:0005886 / monoatomic cation transmembrane transport / potassium ion binding / potassium ion transmembrane transport / potassium ion transport / hydrolase activity / magnesium ion binding / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||||||||
![]() | Silberberg JM / Corey RA | ||||||||||||||||||
Funding support | ![]() ![]() ![]()
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![]() | ![]() Title: Deciphering ion transport and ATPase coupling in the intersubunit tunnel of KdpFABC. Authors: Jakob M Silberberg / Robin A Corey / Lisa Hielkema / Charlott Stock / Phillip J Stansfeld / Cristina Paulino / Inga Hänelt / ![]() ![]() ![]() ![]() Abstract: KdpFABC, a high-affinity K pump, combines the ion channel KdpA and the P-type ATPase KdpB to secure survival at K limitation. Here, we apply a combination of cryo-EM, biochemical assays, and MD ...KdpFABC, a high-affinity K pump, combines the ion channel KdpA and the P-type ATPase KdpB to secure survival at K limitation. Here, we apply a combination of cryo-EM, biochemical assays, and MD simulations to illuminate the mechanisms underlying transport and the coupling to ATP hydrolysis. We show that ions are transported via an intersubunit tunnel through KdpA and KdpB. At the subunit interface, the tunnel is constricted by a phenylalanine, which, by polarized cation-π stacking, controls K entry into the canonical substrate binding site (CBS) of KdpB. Within the CBS, ATPase coupling is mediated by the charge distribution between an aspartate and a lysine. Interestingly, individual elements of the ion translocation mechanism of KdpFABC identified here are conserved among a wide variety of P-type ATPases from different families. This leads us to the hypothesis that KdpB might represent an early descendant of a common ancestor of cation pumps. #1: ![]() Title: Deciphering ion transport and ATPase coupling in the intersubunit tunnel of KdpFABC Authors: Silberberg JM / Corey RA / Hielkema L / Stock C / Stansfeld PJ / Paulino C / Hanelt I | ||||||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 49.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 26.1 KB 26.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.6 KB | Display | ![]() |
Images | ![]() | 106.7 KB | ||
Masks | ![]() | 52.7 MB | ![]() | |
Filedesc metadata | ![]() | 9 KB | ||
Others | ![]() ![]() | 40.7 MB 40.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7nnpMC ![]() 7nnlC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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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 | Rb-loaded E1-ATP map of the KdpFABC complex at 3.2 A resolution sharpened at -130 A2. Data obtained in the presence of 100 mM RbCl, 1 mM ATP, 10 mM AMPPCP. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.012 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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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_12482_half_map_1.map | ||||||||||||
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Annotation | Half map 1 used during refinement and for FSC gold-standard calculation Rb-loaded E1-ATP KdpFABC. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2 used during refinement and for...
File | emd_12482_half_map_2.map | ||||||||||||
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Annotation | Half map 2 used during refinement and for FSC gold-standard calculation Rb-loaded E1-ATP KdpFABC. | ||||||||||||
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: ![]() ![]() |
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: 59.276652 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 GTNDGGFFNA 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 UniProtKB: Potassium-transporting ATPase potassium-binding subunit |
-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 UniProtKB: Potassium-transporting ATPase KdpC subunit |
-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 UniProtKB: Potassium-transporting ATPase KdpF subunit |
-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: 72.251867 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSRKQLALFE PTLVVQALKE AVKKLNPQAQ WRNPVMFIVW IGSLLTTCIS IAMASGAMPG NALFSAAISG WLWITVLFAN FAEALAEGR SKAQANSLKG VKKTAFARKL REPKYGAAAD KVPADQLRKG DIVLVEAGDI IPCDGEVIEG GASVDESAIT G EAAPVIRE ...String: MSRKQLALFE PTLVVQALKE AVKKLNPQAQ WRNPVMFIVW IGSLLTTCIS IAMASGAMPG NALFSAAISG WLWITVLFAN FAEALAEGR SKAQANSLKG VKKTAFARKL REPKYGAAAD KVPADQLRKG DIVLVEAGDI IPCDGEVIEG GASVDESAIT G EAAPVIRE SGGDFASVTG GTRILSDWLV IECSVNPGET FLDRMIAMVE GAQRRKTPNE IALTILLIAL TIVFLLATAT LW PFSAWGG NAVSVTVLVA LLVCLIPTTI GGLLSAIGVA GMSRMLGANV IATSGRAVEA AGDVDVLLLD KTGTITLGNR QAS EFIPAQ GVDEKTLADA AQLASLADET PEGRSIVILA KQRFNLRERD VQSLHATFVP FTAQSRMSGI NIDNRMIRKG SVDA IRRHV EANGGHFPTD VDQKVDQVAR QGATPLVVVE GSRVLGVIAL KDIVKGGIKE RFAQLRKMGI KTVMITGDNR LTAAA IAAE AGVDDFLAEA TPEAKLALIR QYQAEGRLVA MTGDGTNDAP ALAQADVAVA MNSGTQAAKE AGNMVDLDSN PTKLIE VVH IGKQMLMTRG SLTTFSIAND VAKYFAIIPA AFAATYPQLN ALNIMCLHSP DSAILSAVIF NALIIVFLIP LALKGVS YK PLTASAMLRR NLWIYGLGGL LVPFIGIKVI DLLLTVCGLV UniProtKB: Potassium-transporting ATPase ATP-binding subunit |
-Macromolecule #5: RUBIDIUM ION
Macromolecule | Name: RUBIDIUM ION / type: ligand / ID: 5 / Number of copies: 8 / Formula: RB |
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Molecular weight | Theoretical: 85.468 Da |
Chemical component information | ![]() ChemComp-RB: |
-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: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
Macromolecule | Name: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / type: ligand / ID: 7 / Number of copies: 1 / Formula: ACP |
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Molecular weight | Theoretical: 505.208 Da |
Chemical component information | ![]() ChemComp-ACP: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 4.0 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 / Pretreatment - Time: 20 sec. / 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: 8 / Number real images: 22046 / 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 |