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- EMDB-6799: PIG GASTRIC H+,K+ - ATPASE IN COMPLEX with BYK99 -

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Basic information

Entry
Database: EMDB / ID: 6799
TitlePIG GASTRIC H+,K+ - ATPASE IN COMPLEX with BYK99
Map data
SamplePIG GASTRIC H+/ K+ - ATPASE IN COMPLEX WITH BYK99
  • (Potassium-transporting ATPase ...) x 2
Function / homologyP-type ATPase, A domain superfamily / HAD-like superfamily / P-type ATPase, phosphorylation site / Gastric H+/K+-transporter P-type ATPase, N-terminal / P-type ATPase, cytoplasmic domain N / Cation-transporting P-type ATPase, C-terminal / P-type ATPase subfamily IIC, subunit alpha / Cation-transporting P-type ATPase, N-terminal / P-type ATPase / Sodium/potassium-transporting ATPase subunit beta ...P-type ATPase, A domain superfamily / HAD-like superfamily / P-type ATPase, phosphorylation site / Gastric H+/K+-transporter P-type ATPase, N-terminal / P-type ATPase, cytoplasmic domain N / Cation-transporting P-type ATPase, C-terminal / P-type ATPase subfamily IIC, subunit alpha / Cation-transporting P-type ATPase, N-terminal / P-type ATPase / Sodium/potassium-transporting ATPase subunit beta / Sodium/potassium-transporting ATPase subunit beta superfamily / P-type ATPase, transmembrane domain superfamily / Sodium / potassium ATPase beta chain / Cation transporting ATPase, C-terminus / Cation transporter/ATPase, N-terminus / Gastric H+/K+-ATPase, N terminal domain / E1-E2 ATPases phosphorylation site. / Sodium and potassium ATPases beta subunits signature 1. / Sodium and potassium ATPases beta subunits signature 2. / Ion transport by P-type ATPases / HAD superfamily / H+/K+-exchanging ATPase / potassium:proton exchanging ATPase activity / sodium:potassium-exchanging ATPase complex / sodium:potassium-exchanging ATPase activity / sodium ion transport / ATP hydrolysis coupled proton transport / potassium ion transport / cell adhesion / magnesium ion binding / integral component of membrane / ATP binding / plasma membrane / Potassium-transporting ATPase subunit beta / Potassium-transporting ATPase alpha chain 1
Function and homology information
SourceSus scrofa (pig)
Methodelectron crystallography / cryo EM / 6.5 Å resolution
AuthorsAbe K / Shimokawa J
CitationJournal: Sci Rep / Year: 2017
Title: The cryo-EM structure of gastric H,K-ATPase with bound BYK99, a high-affinity member of K-competitive, imidazo[1,2-a]pyridine inhibitors.
Authors: Kazuhiro Abe / Jun Shimokawa / Mao Naito / Keith Munson / Olga Vagin / George Sachs / Hiroshi Suzuki / Kazutoshi Tani / Yoshinori Fujiyoshi
Validation ReportPDB-ID: 5y0b

SummaryFull reportAbout validation report
DateDeposition: Jul 16, 2017 / Header (metadata) release: Aug 9, 2017 / Map release: Aug 9, 2017 / Last update: Aug 9, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.004
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.004
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5y0b
  • Surface level: 0.004
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5y0b
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6799.map.gz (map file in CCP4 format, 16630 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesY (Sec.)X (Row.)Z (Col.)
105 pix
1.08 Å/pix.
= 111.998 Å
137 pix
1.05 Å/pix.
= 142.596 Å
289 pix
1.11 Å/pix.
= 319.997 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

(generated in cubic-lattice coordinate)

Voxel sizeX: 1.0485 Å / Y: 1.0769 Å / Z: 1.1111 Å
Density
Contour Level:0.004 (by author), 0.004 (movie #1):
Minimum - Maximum-0.01762751 - 0.02270848
Average (Standard dev.)-6.678895E-6 (0.003254603)
Details

EMDB XML:

Space Group Number18
Map Geometry
Axis orderZXY
Dimensions137289105
Origin-68-144-52
Limit6814452
Spacing136104288
CellA: 142.596 Å / B: 111.997604 Å / C: 319.9968 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.04851.07690384615381.1111006944444
M x/y/z136104288
origin x/y/z0.0000.0000.000
length x/y/z142.596111.998319.997
α/β/γ90.00090.00090.000
start NX/NY/NZ-68-52-144
NX/NY/NZ137105289
MAP C/R/S312
start NC/NR/NS-144-68-52
NC/NR/NS289137105
D min/max/mean-0.0180.023-0.000

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Supplemental data

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Sample components

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Entire PIG GASTRIC H+/ K+ - ATPASE IN COMPLEX WITH BYK99

EntireName: PIG GASTRIC H+/ K+ - ATPASE IN COMPLEX WITH BYK99 / Number of components: 3

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Component #1: protein, PIG GASTRIC H+/ K+ - ATPASE IN COMPLEX WITH BYK99

ProteinName: PIG GASTRIC H+/ K+ - ATPASE IN COMPLEX WITH BYK99 / Recombinant expression: No
SourceSpecies: Sus scrofa (pig)
Source (natural)Organ or tissue: stomach

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Component #2: protein, Potassium-transporting ATPase alpha chain 1

ProteinName: Potassium-transporting ATPase alpha chain 1 / Recombinant expression: No
MassTheoretical: 114.399688 kDa
SourceSpecies: Sus scrofa (pig)
Source (natural)Organ or tissue: STOMACH

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Component #3: protein, Potassium-transporting ATPase subunit beta

ProteinName: Potassium-transporting ATPase subunit beta / Recombinant expression: No
MassTheoretical: 33.113844 kDa
SourceSpecies: Sus scrofa (pig)
Source (natural)Organ or tissue: stomach

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Experimental details

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Sample preparation

SpecimenSpecimen state: 2D array / Method: cryo EM
Crystal parametersPlane group: P 2 21 21 / A: 142.6 Å / B: 112 Å / C: 320 Å / Gamma: 90 deg.
Sample solutionSpecimen conc.: 6.5 mg/ml / pH: 4.8
VitrificationInstrument: LEICA KF80 / Cryogen name: NITROGEN

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Electron microscopy imaging

ImagingMicroscope: JEOL KYOTO-3000SFF
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 8 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: KODAK SO-163 FILM

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Image processing

ProcessingMethod: electron crystallography
3D reconstructionSoftware: MRC / Resolution: 6.5 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES

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Atomic model buiding

Output model

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