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- EMDB-1831: Pig Gastric H,K-ATPase with bound BeF and SCH28080 -

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Basic information

Entry
Database: EMDB / ID: EMD-1831
TitlePig Gastric H,K-ATPase with bound BeF and SCH28080
Map dataThis is an image of a surface rendered side view of H,K-ATPase with bound BeF and SCH28080
Sample
  • Sample: Pig Gastric H,K-ATPase
  • Protein or peptide: POTASSIUM-TRANSPORTING ATPASE ALPHA CHAIN 1
  • Protein or peptide: POTASSIUM-TRANSPORTING ATPASE SUBUNIT BETA
KeywordsION PUMP / H/K-ATPASE / P-TYPE ATPASE / MEMBRANE PROTEIN / BERYLLIUM FLUORIDE / ATP-BINDING / ACID SUPPRESSANT
Function / homology
Function and homology information


proton transmembrane transport => GO:1902600 / Basigin interactions / Ion homeostasis / H+/K+-exchanging ATPase / potassium:proton exchanging ATPase complex / positive regulation of P-type sodium:potassium-exchanging transporter activity / P-type potassium:proton transporter activity / positive regulation of sodium ion export across plasma membrane / positive regulation of potassium ion import across plasma membrane / Ion transport by P-type ATPases ...proton transmembrane transport => GO:1902600 / Basigin interactions / Ion homeostasis / H+/K+-exchanging ATPase / potassium:proton exchanging ATPase complex / positive regulation of P-type sodium:potassium-exchanging transporter activity / P-type potassium:proton transporter activity / positive regulation of sodium ion export across plasma membrane / positive regulation of potassium ion import across plasma membrane / Ion transport by P-type ATPases / P-type sodium:potassium-exchanging transporter activity / sodium:potassium-exchanging ATPase complex / membrane repolarization / ATP biosynthetic process / establishment or maintenance of transmembrane electrochemical gradient / sodium ion export across plasma membrane / intracellular potassium ion homeostasis / intracellular sodium ion homeostasis / potassium ion import across plasma membrane / potassium ion binding / ATPase activator activity / potassium ion transmembrane transport / proton transmembrane transport / potassium ion transport / sarcolemma / transmembrane transport / ATPase binding / protein-macromolecule adaptor activity / cell adhesion / apical plasma membrane / innate immune response / 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 ...: / : / 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
Sodium/potassium-transporting ATPase subunit beta-1 / Potassium-transporting ATPase subunit beta / Potassium-transporting ATPase alpha chain 1
Similarity search - Component
Biological speciesSus scrofa (pig)
Methodelectron crystallography / cryo EM / Resolution: 7.0 Å
AuthorsAbe K / Tani K / Fujiyoshi Y
CitationJournal: Nat Commun / Year: 2011
Title: Conformational rearrangement of gastric H(+),K(+)-ATPase induced by an acid suppressant.
Authors: Kazuhiro Abe / Kazutoshi Tani / Yoshinori Fujiyoshi /
Abstract: Acid-related gastric diseases are associated with disorder of digestive tract acidification. The gastric proton pump, H(+),K(+)-ATPase, exports H(+) in exchange for luminal K(+) to generate a highly ...Acid-related gastric diseases are associated with disorder of digestive tract acidification. The gastric proton pump, H(+),K(+)-ATPase, exports H(+) in exchange for luminal K(+) to generate a highly acidic environment in the stomach, and is a main target for acid suppressants. Here, we report the three-dimensional structure of gastric H(+),K(+)-ATPase with bound SCH28080, a representative K(+)-competitive acid blocker, at 7 Å resolution based on electron crystallography of two-dimensional crystals. The density of the bound SCH28080 is found near transmembrane (TM) helices 4, 5 and 6, in the luminal cavity. The SCH28080-binding site is formed by the rearrangement of TM helices, which is in turn transmitted to the cytoplasmic domains, resulting in a luminal-open conformation. These results represent the first structural evidence for a binding site of an acid suppressant on H(+),K(+)-ATPase, and the conformational change induced by this class of drugs.
History
DepositionNov 24, 2010-
Header (metadata) releaseJun 7, 2011-
Map releaseJun 7, 2011-
UpdateSep 25, 2013-
Current statusSep 25, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-2xzb
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-2xzb
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_1831.png

Downloads & links

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Map

FileDownload / File: emd_1831.map.gz / Format: CCP4 / Size: 1.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is an image of a surface rendered side view of H,K-ATPase with bound BeF and SCH28080
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesY (Sec.)X (Row.)Z (Col.)
2.32 Å/pix.
x 49 pix.
= 111.36 Å		2.35 Å/pix.
x 61 pix.
= 141. Å		2.29 Å/pix.
x 141 pix.
= 320.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX: 2.35 Å / Y: 2.32 Å / Z: 2.29 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.035 / Movie #1: 0.06
Minimum - Maximum-0.10629842 - 0.16671327
Average (Standard dev.)-0.0001365 (±0.02382653)
SymmetrySpace group: 18
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin-30-70-24
Dimensions6114149
Spacing4860140
CellA: 141.0 Å / B: 111.36 Å / C: 320.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.352.322.29
M x/y/z6048140
origin x/y/z0.0000.0000.000
length x/y/z141.000111.360320.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-30-24-70
NX/NY/NZ6149141
MAP C/R/S312
start NC/NR/NS-70-30-24
NC/NR/NS1416149
D min/max/mean-0.1060.167-0.000

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Supplemental data

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Sample components

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Entire : Pig Gastric H,K-ATPase

EntireName: Pig Gastric H,K-ATPase
Components
  • Sample: Pig Gastric H,K-ATPase
  • Protein or peptide: POTASSIUM-TRANSPORTING ATPASE ALPHA CHAIN 1
  • Protein or peptide: POTASSIUM-TRANSPORTING ATPASE SUBUNIT BETA

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Supramolecule #1000: Pig Gastric H,K-ATPase

SupramoleculeName: Pig 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 ALPHA CHAIN 1

MacromoleculeName: POTASSIUM-TRANSPORTING ATPASE ALPHA CHAIN 1 / type: protein_or_peptide / ID: 1 / Name.synonym: Gastric proton pump / Number of copies: 1 / 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
SequenceUniProtKB: Potassium-transporting ATPase alpha chain 1
GO: 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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Macromolecule #2: POTASSIUM-TRANSPORTING ATPASE SUBUNIT BETA

MacromoleculeName: POTASSIUM-TRANSPORTING ATPASE SUBUNIT BETA / type: protein_or_peptide / ID: 2 / Name.synonym: Gastric proton pump / Number of copies: 1 / 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
SequenceUniProtKB: Sodium/potassium-transporting ATPase subunit beta-1
GO: 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

Concentration8 mg/mL
BufferpH: 5.5
Details: 20mM MES, 20mM Mg(CH3COO)2, 5mM ATP, 10%(v/v) glycerol, 3mM DTT
VitrificationCryogen name: NITROGEN / Chamber temperature: 100 K / Instrument: REICHERT-JUNG PLUNGER
Details: Vitrification instrument: Reichert plunger. Vitrification carried out in cold room at 4 degrees celsius
Method: Carbon sandwich preparation
DetailsCrystal grown in dialysis
Crystal formationDetails: Crystal grown in dialysis

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Electron microscopy

MicroscopeJEOL KYOTO-3000SFF
TemperatureAverage: 4.5 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 400,000 times magnification
DateMar 29, 2010
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 515 / Average electron dose: 25 e/Å2 / Bits/pixel: 12
Tilt angle min0
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.6 mm / Nominal defocus max: 4.13 µm / Nominal defocus min: 0.58 µm / Nominal magnification: 40000
Sample stageSpecimen holder: Top entry / Specimen holder model: JEOL / Tilt angle max: 64 / Tilt series - Axis1 - Min angle: 0 ° / Tilt series - Axis1 - Max angle: 64.0 °

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.0 Å / Resolution method: OTHER / Software - Name: MRC
Crystal parametersUnit cell - A: 140.9 Å / Unit cell - B: 111.3 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

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Atomic model buiding 1

Initial modelPDB ID:

3a3y

RefinementSpace: REAL
Output model

PDB-2xzb:
Pig Gastric H,K-ATPase with bound BeF and SCH28080

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