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- EMDB-5104: Gastric H,K-ATPase complexed with aluminum fluoride -

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Basic information

Entry
Database: EMDB / ID: EMD-5104
TitleGastric H,K-ATPase complexed with aluminum fluoride
Map datagastric HK-ATPase complexed with aluminium fluoride
Sample
  • Sample: Gastric H,K-ATPase
  • Protein or peptide: Potassium-transporting ATPase
KeywordsION PUMP / H+ / K+-ATPASE / P-TYPE ATPASE / MEMBRANE PROTEIN / HYDROLASE / E2 / ALUMINUM FLUORIDE
Function / homology
Function and homology information


proton transmembrane transport => GO:1902600 / H+/K+-exchanging ATPase / potassium:proton exchanging ATPase complex / P-type potassium:proton transporter activity / Ion transport by P-type ATPases / P-type sodium:potassium-exchanging transporter activity / ATP biosynthetic process / sodium:potassium-exchanging ATPase complex / sodium ion export across plasma membrane / intracellular potassium ion homeostasis ...proton transmembrane transport => GO:1902600 / H+/K+-exchanging ATPase / potassium:proton exchanging ATPase complex / P-type potassium:proton transporter activity / Ion transport by P-type ATPases / P-type sodium:potassium-exchanging transporter activity / ATP biosynthetic process / sodium:potassium-exchanging ATPase complex / sodium ion export across plasma membrane / intracellular potassium ion homeostasis / intracellular sodium ion homeostasis / potassium ion import across plasma membrane / ATPase activator activity / potassium ion binding / potassium ion transmembrane transport / proton transmembrane transport / potassium ion transport / cell adhesion / apical plasma membrane / magnesium ion binding / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
: / : / Gastric H+/K+-transporter P-type ATPase, N-terminal / Gastric H+/K+-transporter P-type ATPase, N-terminal / Gastric H+/K+-ATPase, N terminal domain / Sodium/potassium-transporting ATPase subunit beta / 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. ...: / : / Gastric H+/K+-transporter P-type ATPase, N-terminal / Gastric H+/K+-transporter P-type ATPase, N-terminal / Gastric H+/K+-ATPase, N terminal domain / Sodium/potassium-transporting ATPase subunit beta / 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 / P-type ATPase subfamily IIC, subunit alpha / Cation-transporting P-type ATPase, C-terminal / 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-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, A domain superfamily / P-type ATPase / P-type ATPase / P-type ATPase, transmembrane domain superfamily / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Potassium-transporting ATPase subunit beta / Potassium-transporting ATPase alpha chain 1
Similarity search - Component
Biological speciesSus scrofa (pig)
Methodelectron crystallography / cryo EM / Resolution: 6.5 Å
AuthorsAbe K / Tani K / Nishizawa T / Fujiyoshi Y
CitationJournal: EMBO J / Year: 2009
Title: Inter-subunit interaction of gastric H+,K+-ATPase prevents reverse reaction of the transport cycle.
Authors: Kazuhiro Abe / Kazutoshi Tani / Tomohiro Nishizawa / Yoshinori Fujiyoshi /
Abstract: The gastric H(+),K(+)-ATPase is an ATP-driven proton pump responsible for generating a million-fold proton gradient across the gastric membrane. We present the structure of gastric H(+),K(+)-ATPase ...The gastric H(+),K(+)-ATPase is an ATP-driven proton pump responsible for generating a million-fold proton gradient across the gastric membrane. We present the structure of gastric H(+),K(+)-ATPase at 6.5 A resolution as determined by electron crystallography of two-dimensional crystals. The structure shows the catalytic alpha-subunit and the non-catalytic beta-subunit in a pseudo-E(2)P conformation. Different from Na(+),K(+)-ATPase, the N-terminal tail of the beta-subunit is in direct contact with the phosphorylation domain of the alpha-subunit. This interaction may hold the phosphorylation domain in place, thus stabilizing the enzyme conformation and preventing the reverse reaction of the transport cycle. Indeed, truncation of the beta-subunit N-terminus allowed the reverse reaction to occur. These results suggest that the beta-subunit N-terminus prevents the reverse reaction from E(2)P to E(1)P, which is likely to be relevant for the generation of a large H(+) gradient in vivo situation.
History
DepositionMar 9, 2009-
Header (metadata) releaseMar 24, 2009-
Map releaseMay 22, 2009-
UpdateDec 26, 2012-
Current statusDec 26, 2012Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0023
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  • Surface view colored by height
  • Surface level: 0.0023
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  • Surface view with fitted model
  • Atomic models: PDB-3ixz
  • Surface level: 0.0023
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  • Surface view with fitted model
  • Atomic models: PDB-3ixz
  • Surface level: 0.0023
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3ixz
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5104_1.png

Downloads & links

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Map

FileDownload / File: emd_5104.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationgastric HK-ATPase complexed with aluminium fluoride
Voxel sizeX: 2.06471 Å / Y: 2.09615 Å / Z: 2.22222 Å
Density
Contour LevelBy EMDB: 0.0015 / Movie #1: 0.0023
Minimum - Maximum-0.00829937 - 0.01014665
Average (Standard dev.)-0.00000501 (±0.00140999)
SymmetrySpace group: 18
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin-34-72-26
Dimensions6914553
Spacing5268144
CellA: 140.40027 Å / B: 108.999794 Å / C: 319.99966 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.06470588235292.09615384615382.2222222222222
M x/y/z6852144
origin x/y/z0.0000.0000.000
length x/y/z140.400109.000320.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S312
start NC/NR/NS-72-34-26
NC/NR/NS1456953
D min/max/mean-0.0080.010-0.000

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Supplemental data

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Segmentation: HK-ATPase

AnnotationHK-ATPase
Fileemd_5104_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Gastric H,K-ATPase

EntireName: Gastric H,K-ATPase
Components
  • Sample: Gastric H,K-ATPase
  • Protein or peptide: Potassium-transporting ATPase

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Supramolecule #1000: Gastric H,K-ATPase

SupramoleculeName: Gastric H,K-ATPase / type: sample / ID: 1000 / Oligomeric state: one alpha and one beta chain of HK-ATPase / Number unique components: 2
Molecular weightTheoretical: 150 KDa

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Macromolecule #1: Potassium-transporting ATPase

MacromoleculeName: Potassium-transporting ATPase / type: protein_or_peptide / ID: 1 / Name.synonym: HK-ATPase / Number of copies: 2 / Oligomeric state: dimer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Sus scrofa (pig) / synonym: Pig / Tissue: stomach / Location in cell: plasma membrane
Molecular weightTheoretical: 150 KDa
SequenceGO: ATP biosynthetic process, proton transmembrane transport => GO:1902600, potassium ion transport
InterPro: P-type ATPase, A domain superfamily, P-type ATPase subfamily IIC, subunit alpha, INTERPRO: IPR006069, Cation-transporting P-type ATPase, C-terminal, Cation-transporting P-type ATPase, N- ...InterPro: P-type ATPase, A domain superfamily, P-type ATPase subfamily IIC, subunit alpha, INTERPRO: IPR006069, Cation-transporting P-type ATPase, C-terminal, Cation-transporting P-type ATPase, N-terminal, Gastric H+/K+-transporter P-type ATPase, N-terminal, P-type ATPase, INTERPRO: IPR005834, Sodium/potassium-transporting ATPase subunit beta

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron crystallography
Aggregation state2D array

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Sample preparation

Concentration2.5 mg/mL
BufferpH: 4.87
Details: 20 mM propionate, 1 mM MgCl2, 0.5 mM AlCl3, 4 mM NaF, 0.3 mM ADP, 3 mM DTT, 10% (w/v) glycerol
GridDetails: molybdenum grid
VitrificationCryogen name: NITROGEN / Chamber temperature: 4.2 K / Instrument: REICHERT-JUNG PLUNGER
Details: Vitrification instrument: Reichert plunger. vitrification carried out in cold room at 4 degrees celsius.
Method: carbon sandwich preparation
Detailsdialysis
Crystal formationDetails: dialysis

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Electron microscopy

MicroscopeJEOL KYOTO-3000SFF
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 59100 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 1.6 mm / Nominal defocus max: 3.48 µm / Nominal defocus min: 0.39 µm / Nominal magnification: 60000
Sample stageSpecimen holder: top entry / Specimen holder model: JEOL / Tilt angle max: 73.3 / Tilt series - Axis1 - Min angle: 0 ° / Tilt series - Axis1 - Max angle: 73.3 °
TemperatureAverage: 4.2 K
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 346 / Average electron dose: 25 e/Å2 / Bits/pixel: 12
Tilt angle min0

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Image processing

Crystal parametersUnit cell - A: 140.4 Å / Unit cell - B: 109.0 Å / Unit cell - C: 320.0 Å / Unit cell - γ: 90.0 ° / Unit cell - α: 90.0 ° / Unit cell - β: 90.0 ° / Plane group: P 2 21 21
CTF correctionDetails: Each image
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.5 Å / Resolution method: OTHER / Software - Name: MRC

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