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- EMDB-35488: Cyo-EM structure of wildtype non-gastric proton pump in the prese... -

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Basic information

Entry
Database: EMDB / ID: EMD-35488
TitleCyo-EM structure of wildtype non-gastric proton pump in the presence of Na+, AlF and ADP
Map data
Sample
  • Complex: hetero dimer of alpha and beta subunit
    • Protein or peptide: x 2 types
  • Ligand: x 9 types
KeywordsP-type ATPase / P2-type ATPase / MEMBRANE PROTEIN
Function / homology
Function and homology information


Ion transport by P-type ATPases / P-type potassium:proton transporter activity / positive regulation of sodium ion export across plasma membrane / positive regulation of potassium ion import across plasma membrane / metal ion transport / P-type sodium:potassium-exchanging transporter activity / membrane repolarization / sodium:potassium-exchanging ATPase complex / sodium ion export across plasma membrane / regulation of calcium ion transmembrane transport ...Ion transport by P-type ATPases / P-type potassium:proton transporter activity / positive regulation of sodium ion export across plasma membrane / positive regulation of potassium ion import across plasma membrane / metal ion transport / P-type sodium:potassium-exchanging transporter activity / membrane repolarization / sodium:potassium-exchanging ATPase complex / sodium ion export across plasma membrane / regulation of calcium ion transmembrane transport / intracellular potassium ion homeostasis / regulation of pH / intracellular sodium ion homeostasis / potassium ion homeostasis / regulation of cardiac muscle contraction by calcium ion signaling / relaxation of cardiac muscle / Ion homeostasis / sodium ion transport / potassium ion import across plasma membrane / ATPase activator activity / monoatomic cation transmembrane transport / blastocyst development / organelle membrane / intercalated disc / sodium ion transmembrane transport / lateral plasma membrane / sperm flagellum / ATP metabolic process / cardiac muscle contraction / T-tubule / caveola / protein localization to plasma membrane / sarcolemma / potassium ion transport / intracellular calcium ion homeostasis / protein-macromolecule adaptor activity / ATPase binding / regulation of gene expression / basolateral plasma membrane / response to hypoxia / protein stabilization / cell adhesion / apical plasma membrane / protein heterodimerization activity / innate immune response / protein kinase binding / ATP hydrolysis activity / ATP binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Sodium/potassium-transporting ATPase subunit beta / Sodium/potassium-transporting ATPase subunit beta superfamily / Sodium / potassium ATPase beta chain / Sodium and potassium ATPases beta subunits signature 1. / Sodium and potassium ATPases beta subunits signature 2. / P-type ATPase subfamily IIC, subunit alpha / Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal ...Sodium/potassium-transporting ATPase subunit beta / Sodium/potassium-transporting ATPase subunit beta superfamily / Sodium / potassium ATPase beta chain / Sodium and potassium ATPases beta subunits signature 1. / Sodium and potassium ATPases beta subunits signature 2. / P-type ATPase subfamily IIC, subunit alpha / Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / Cation transport ATPase (P-type) / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Sodium/potassium-transporting ATPase subunit alpha / Sodium/potassium-transporting ATPase subunit beta-1
Similarity search - Component
Biological speciesRattus (rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.62 Å
AuthorsAbe K
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21H02426 Japan
CitationJournal: Biochim Biophys Acta Mol Cell Res / Year: 2023
Title: An unusual conformation from Na-sensitive non-gastric proton pump mutants reveals molecular mechanisms of cooperative Na-binding.
Authors: Kazuhiro Abe / Tomohiro Nishizawa / Pablo Artigas /
Abstract: The Na,K-ATPase (NKA) and non-gastric H,K- ATPase (ngHKA) share ~65 % sequence identity, and nearly identical catalytic cycles. These pumps alternate between inward-facing (E1) and outward-facing ...The Na,K-ATPase (NKA) and non-gastric H,K- ATPase (ngHKA) share ~65 % sequence identity, and nearly identical catalytic cycles. These pumps alternate between inward-facing (E1) and outward-facing (E2) conformations and differ in their exported substrate (Na or H) and stoichiometries (3 Na:2 K or 1 H:1 K). We reported that structures of the NKA-mimetic ngHKA mutant K794S/A797P/W940/R949C (SPWC) with 2 K occluded in E2-P and 3 Na-bound in E1·ATP states were nearly identical to NKA structures in equivalent states. Here we report the cryo-EM structures of K794A and K794S, two poorly-selective ngHKA mutants, under conditions to stabilize the E1·ATP state. Unexpectedly, the structures show a hybrid with both E1- and E2-like structural features. While transmembrane segments TM1-TM3 and TM4's extracellular half adopted an E2-like conformation, the rest of the protein assumed an E1 configuration. Two spherical densities, likely bound Na, were observed at cation-binding sites I and III, without density at site II. This explains the E2-like conformation of TM4's exoplasmic half. In NKA, oxygen atoms derived from the unwound portion of TM4 coordinated Na at site II. Thus, the lack of Na at site II of K794A/S prevents the luminal portion of TM4 from taking an E1-like position. The K794A structure also suggests that incomplete coordination of Na at site III induces the halfway rotation of TM6, which impairs Na-binding at the site II. Thus, our observations provide insight into the molecular mechanism of E2-E1 transition and cooperative Na-binding in the NKA and other related cation pumps.
History
DepositionFeb 27, 2023-
Header (metadata) releaseOct 18, 2023-
Map releaseOct 18, 2023-
UpdateOct 18, 2023-
Current statusOct 18, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35488.png

Downloads & links

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Map

FileDownload / File: emd_35488.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.227
Minimum - Maximum-1.4797734 - 2.2804306
Average (Standard dev.)-0.0003037011 (±0.034385774)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 348.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_35488_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35488_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: #2

Fileemd_35488_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : hetero dimer of alpha and beta subunit

EntireName: hetero dimer of alpha and beta subunit
Components
  • Complex: hetero dimer of alpha and beta subunit
    • Protein or peptide: Sodium/potassium-transporting ATPase subunit alpha
    • Protein or peptide: Sodium/potassium-transporting ATPase subunit beta-1
  • Ligand: TETRAFLUOROALUMINATE ION
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: CHOLESTEROL
  • Ligand: SODIUM IONSodium
  • Ligand: 2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

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Supramolecule #1: hetero dimer of alpha and beta subunit

SupramoleculeName: hetero dimer of alpha and beta subunit / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Rattus (rat)
Molecular weightTheoretical: 135 kDa/nm

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Macromolecule #1: Sodium/potassium-transporting ATPase subunit alpha

MacromoleculeName: Sodium/potassium-transporting ATPase subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus (rat)
Molecular weightTheoretical: 109.084688 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GMDLDDHRLS NTELEQKYGT NIIQGLSSVR ATELLARDGP NTLTPPKQTP EIIKFLKQMV GGFSILLWIG AALCWIAFVI QYVNNSASL DNVYLGAILV LVVILTGIFA YYQEAKSTNI MASFSKMIPQ QALVIRDAEK KVISAEQLVV GDVVEIKGGD Q IPADIRLV ...String:
GMDLDDHRLS NTELEQKYGT NIIQGLSSVR ATELLARDGP NTLTPPKQTP EIIKFLKQMV GGFSILLWIG AALCWIAFVI QYVNNSASL DNVYLGAILV LVVILTGIFA YYQEAKSTNI MASFSKMIPQ QALVIRDAEK KVISAEQLVV GDVVEIKGGD Q IPADIRLV FSQGCKVDNS SLTGESEPQA RSTEFTHENP LETKNIGFYS TTCLEGTATG IVINTGDRTI IGRIASLASG VG SEKTPIA IEIEHFVHIV AGVAVSIGII FFITAVCMKY YVLDAIIFLI SIIVANVPEG LLATVTVTLS LTAKRMAKKN CLV KNLEAV ETLGSTSIIC SDKTGTLTQN RMTVAHLWFD NQIFVADTSE NQTKQAFDQS SGTWASLSKI ITLCNRAEFR PGQE SVPIM KRTVVGDASE TALLKFSEVI LGDVMGIRKR NHKVAEIPFN STNKFQLSIH ETEDPNNKRF LVVMKGAPER ILEKC STIM INGQEQPLDK SSADSFHTAY MELGGLGERV LGFCHLYLPA EQFPQSYIFD VDSVNFPTSN FCFVGLLSMI DPPRST VPD AVSKCRSAGI KVIMVTGDHP ITAKAIAKSV GIISANNETV EDIAKRRNIA VEQVNKREAK AAVVTGMELK DMTPEQL DE LLTNYQEIVF ARTSPQQKLI IVEGCQRQDA IVAVTGDGVN DSPALKKADI GIAMGIAGSD AAKNAADMVL LDDNFASI V TGVEEGRLIF DNLKKTIAYT LTKNIAELCP FLIYIVAGLP LPIGTITILF IDLGTDIIPS IALAYEKAES DIMNRKPRH KKKDRLVNTQ LAIYSYLHIG LMQALGGFLV YFTVYAQQGF WPTSLINLRV AWETDDINDL EDSYGQEWTR YQRKYLEWTG STAFFVAIM IQQIADLIIR KTRRNSIFQQ GLFRNKVIWV GIASQVIVAL ILSYGLGSVP ALSFTMLRVQ YWFVAVPHAI L IWVYDEMR KLFIRLYPGS WWDKNMYY

UniProtKB: Sodium/potassium-transporting ATPase subunit alpha

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Macromolecule #2: Sodium/potassium-transporting ATPase subunit beta-1

MacromoleculeName: Sodium/potassium-transporting ATPase subunit beta-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus (rat)
Molecular weightTheoretical: 37.516859 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGDYKDDDDK SSGENLYFQG MARGKAKEEG SWKKFIWNSE KKEFLGRTGG SWFKILLFYV IFYGCLAGIF IGTIQVMLLT ISELKPTYQ DRVAPPGLTQ IPQIQKTEIS FRPNDPKSYE AYVLNIIRFL EKYKDSAQKD DMIFEDCGSM PSEPKERGEF N HERGERKV ...String:
MGDYKDDDDK SSGENLYFQG MARGKAKEEG SWKKFIWNSE KKEFLGRTGG SWFKILLFYV IFYGCLAGIF IGTIQVMLLT ISELKPTYQ DRVAPPGLTQ IPQIQKTEIS FRPNDPKSYE AYVLNIIRFL EKYKDSAQKD DMIFEDCGSM PSEPKERGEF N HERGERKV CRFKLDWLGN CSGLNDESYG YKEGKPCIII KLNRVLGFKP KPPKNESLET YPLTMKYNPN VLPVQCTGKR DE DKDKVGN IEYFGMGGFY GFPLQYYPYY GKLLQPKYLQ PLLAVQFTNL TLDTEIRIEC KAYGENIGYS EKDRFQGRFD VKI EVKS

UniProtKB: Sodium/potassium-transporting ATPase subunit beta-1

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Macromolecule #3: TETRAFLUOROALUMINATE ION

MacromoleculeName: TETRAFLUOROALUMINATE ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ALF
Molecular weightTheoretical: 102.975 Da
Chemical component information

ChemComp-ALF:
TETRAFLUOROALUMINATE ION

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

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Macromolecule #6: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 6 / Number of copies: 5 / Formula: PCW
Molecular weightTheoretical: 787.121 Da
Chemical component information

ChemComp-PCW:
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DOPC, phospholipid*YM

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Macromolecule #7: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 7 / Number of copies: 2 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL / Cholesterol

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Macromolecule #8: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 8 / Number of copies: 2
Molecular weightTheoretical: 22.99 Da

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Macromolecule #9: 2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl...

MacromoleculeName: 2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside
type: ligand / ID: 9 / Number of copies: 4 / Formula: Q7G
Molecular weightTheoretical: 1.165315 KDa
Chemical component information

ChemComp-Q7G:
2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside

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Macromolecule #10: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 10 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Macromolecule #11: water

MacromoleculeName: water / type: ligand / ID: 11 / Number of copies: 8 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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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

Concentration8 mg/mL
BufferpH: 6.5
VitrificationCryogen name: ETHANE

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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: 1.8 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 53.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7x20

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 224740
FSC plot (resolution estimation)

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