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Yorodumi- EMDB-33602: Cryo-EM structure of the Na+,K+-ATPase in the E2.2K+ state after ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33602 | |||||||||||||||||||||
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Title | Cryo-EM structure of the Na+,K+-ATPase in the E2.2K+ state after addition of ATP | |||||||||||||||||||||
Map data | ||||||||||||||||||||||
Sample |
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Function / homology | Function and homology information regulation of monoatomic ion transport / P-type potassium transmembrane transporter activity / sodium:potassium-exchanging ATPase complex / ion channel regulator activity / sodium ion transport / monoatomic ion transport / potassium ion transport / ATP hydrolysis activity / ATP binding / membrane ...regulation of monoatomic ion transport / P-type potassium transmembrane transporter activity / sodium:potassium-exchanging ATPase complex / ion channel regulator activity / sodium ion transport / monoatomic ion transport / potassium ion transport / ATP hydrolysis activity / ATP binding / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||||||||||||||
Biological species | Squalus acanthias (spiny dogfish) / spiny dogfish (spiny dogfish) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.2 Å | |||||||||||||||||||||
Authors | Kanai R / Cornelius F / Vilsen B / Toyoshima C | |||||||||||||||||||||
Funding support | Japan, Denmark, 6 items
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Citation | Journal: FEBS Lett / Year: 2022 Title: Cryo-electron microscopy of Na ,K -ATPase reveals how the extracellular gate locks in the E2·2K state. Authors: Ryuta Kanai / Flemming Cornelius / Bente Vilsen / Chikashi Toyoshima / Abstract: Na ,K -ATPase (NKA) is one of the most important members of the P-type ion-translocating ATPases and plays a pivotal role in establishing electrochemical gradients for Na and K across the cell ...Na ,K -ATPase (NKA) is one of the most important members of the P-type ion-translocating ATPases and plays a pivotal role in establishing electrochemical gradients for Na and K across the cell membrane. Presented here is a 3.3 Å resolution structure of NKA in the E2·2K state solved by cryo-electron microscopy. It is a stable state with two occluded K after transferring three Na into the extracellular medium and releasing inorganic phosphate bound to the cytoplasmic P domain. We describe how the extracellular ion pathway wide open in the E2P state becomes closed and locked in E2·2K , linked to events at the phosphorylation site more than 50 Å away. We also show, although at low resolution, how ATP binding to NKA in E2·2K relaxes the gating machinery and thereby accelerates the transition into the next step, that is, the release of K into the cytoplasm, more than 100 times. | |||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33602.map.gz | 48.4 MB | EMDB map data format | |
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Header (meta data) | emd-33602-v30.xml emd-33602.xml | 23.3 KB 23.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_33602_fsc.xml | 8.6 KB | Display | FSC data file |
Images | emd_33602.png | 112.4 KB | ||
Others | emd_33602_half_map_1.map.gz emd_33602_half_map_2.map.gz | 40.5 MB 40.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33602 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33602 | HTTPS FTP |
-Related structure data
Related structure data | 7y46MC 7y45C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_33602.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.076 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_33602_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33602_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Sodium/potassium-transporting ATPase
Entire | Name: Sodium/potassium-transporting ATPase |
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Components |
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-Supramolecule #1: Sodium/potassium-transporting ATPase
Supramolecule | Name: Sodium/potassium-transporting ATPase / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Squalus acanthias (spiny dogfish) |
-Macromolecule #1: Na, K-ATPase alpha subunit
Macromolecule | Name: Na, K-ATPase alpha subunit / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: spiny dogfish (spiny dogfish) |
Molecular weight | Theoretical: 113.309891 KDa |
Sequence | String: MGKGTASDKY EPAATSENAT KSKKKGKKDK IDKKRDLDEL KKEVSMDDHK LSLDELHNKY GTDLTRGLTN ARAKEILARD GPNSLTPPP TTPEWIKFCR QLFGGFSILL WIGAILCFLA YGIQAATEDE PANDNLYLGV VLSTVVIVTG CFSYYQEAKS S RIMDSFKN ...String: MGKGTASDKY EPAATSENAT KSKKKGKKDK IDKKRDLDEL KKEVSMDDHK LSLDELHNKY GTDLTRGLTN ARAKEILARD GPNSLTPPP TTPEWIKFCR QLFGGFSILL WIGAILCFLA YGIQAATEDE PANDNLYLGV VLSTVVIVTG CFSYYQEAKS S RIMDSFKN MVPQQALVIR DGEKSTINAE FVVAGDLVEV KGGDRIPADL RIISAHGCKV DNSSLTGESE PQTRSPEFSS EN PLETRNI AFFSTNCVEG TARGVVVYTG DRTVMGRIAT LASGLEVGRT PIAIEIEHFI HIITGVAVFL GVSFFILSLI LGY SWLEAV IFLIGIIVAN VPEGLLATVT VCLTLTAKRM ARKNCLVKNL EAVETLGSTS TICSDKTGTL TQNRMTVAHM WFDN QIHEA DTTENQSGAA FDKTSATWSA LSRIAALCNR AVFQAGQDNV PILKRSVAGD ASESALLKCI ELCCGSVQGM RDRNP KIVE IPFNSTNKYQ LSIHENEKSS ESRYLLVMKG APERILDRCS TILLNGAEEP LKEDMKEAFQ NAYLELGGLG ERVLGF CHF ALPEDKYNEG YPFDADEPNF PTTDLCFVGL MAMIDPPRAA VPDAVGKCRS AGIKVIMVTG DHPITAKAIA KGVGIIS EG NETIEDIAAR LNIPIGQVNP RDAKACVVHG SDLKDLSTEV LDDILHYHTE IVFARTSPQQ KLIIVEGCQR QGAIVAVT G DGVNDSPALK KADIGVAMGI SGSDVSKQAA DMILLDDNFA SIVTGVEEGR LIFDNLKKSI AYTLTSNIPE ITPFLVFII GNVPLPLGTV TILCIDLGTD MVPAISLAYE QAESDIMKRQ PRNPKTDKLV NERLISMAYG QIGMIQALGG FFSYFVILAE NGFLPMDLI GKRVRWDDRW ISDVEDSFGQ QWTYEQRKIV EFTCHTSFFI SIVVVQWADL IICKTRRNSI FQQGMKNKIL I FGLFEETA LAAFLSYCPG TDVALRMYPL KPSWWFCAFP YSLIIFLYDE MRRFIIRRSP GGWVEQETYY |
-Macromolecule #2: Na+,K+-ATPase beta subunit
Macromolecule | Name: Na+,K+-ATPase beta subunit / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: spiny dogfish (spiny dogfish) |
Molecular weight | Theoretical: 35.176125 KDa |
Sequence | String: MARGKSKETD GGWKKFLWDS EKKEFLGRTG SSWFKIFLFY LIFYGCLAGI FIGTIQVLLL TLSDFEPKYQ DRVAPPGLSH APYAIKTEI SFSISNPKSY ESFVKSMHKL MDLYNESSQA GNSPFEDCSD TPADYIKRGD LDDSQGQKKA CRFSRMWLKN C SGLDDTTY ...String: MARGKSKETD GGWKKFLWDS EKKEFLGRTG SSWFKIFLFY LIFYGCLAGI FIGTIQVLLL TLSDFEPKYQ DRVAPPGLSH APYAIKTEI SFSISNPKSY ESFVKSMHKL MDLYNESSQA GNSPFEDCSD TPADYIKRGD LDDSQGQKKA CRFSRMWLKN C SGLDDTTY GYAEGKPCVV AKLNRIIGFY PKPLKNTTDL PEELQANYNQ YVLPLRCAAK REEDREKIGS IEYFGLGGYA GF PLQYYPY YGKRLQKKYL QPLLAIQFTN LTQNMELRIE CKVYGENIDY SEKDRFRGRF EVKIEVKS |
-Macromolecule #3: FXYD domain-containing ion transport regulator
Macromolecule | Name: FXYD domain-containing ion transport regulator / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: spiny dogfish (spiny dogfish) |
Molecular weight | Theoretical: 10.195847 KDa |
Sequence | String: MLGAATGLMV LVAVTQGVWA MDPEGPDNDE RFTYDYYRLR VVGLIVAAVL CVIGIIILLA GKCRCKFNQN KRTRSNSGTA TAQHLLQPG EATEC |
-Macromolecule #8: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 8 / Number of copies: 2 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Macromolecule #9: POTASSIUM ION
Macromolecule | Name: POTASSIUM ION / type: ligand / ID: 9 / Number of copies: 6 / Formula: K |
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Molecular weight | Theoretical: 39.098 Da |
-Macromolecule #10: CHOLESTEROL
Macromolecule | Name: CHOLESTEROL / type: ligand / ID: 10 / Number of copies: 8 / Formula: CLR |
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Molecular weight | Theoretical: 386.654 Da |
Chemical component information | ChemComp-CLR: |
-Macromolecule #11: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Macromolecule | Name: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 11 / Number of copies: 2 / Formula: PCW |
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Molecular weight | Theoretical: 787.121 Da |
Chemical component information | ChemComp-PCW: |
-Macromolecule #12: water
Macromolecule | Name: water / type: ligand / ID: 12 / Number of copies: 4 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.5 mg/mL | |||||||||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 20.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | |||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 99.9 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |