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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: EMD-6799
TitlePIG GASTRIC H+,K+ - ATPASE IN COMPLEX with BYK99
Map data
Sample
  • Complex: PIG GASTRIC H+/ K+ - ATPASE IN COMPLEX WITH BYK99
    • Protein or peptide: Potassium-transporting ATPase alpha chain 1
    • Protein or peptide: Potassium-transporting ATPase subunit beta
Function / homology
Function and homology information


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 / 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 ...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 / 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 / potassium ion binding / ATPase activator activity / potassium ion transmembrane transport / proton transmembrane 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+-ATPase, N terminal domain / 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 ...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 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
Potassium-transporting ATPase subunit beta / Potassium-transporting ATPase alpha chain 1
Similarity search - Component
Biological speciesSus scrofa (pig) / Pig (pig)
Methodelectron crystallography / cryo EM / Resolution: 6.5 Å
AuthorsAbe K / Shimokawa J / Natio M / Munson K / Vagin O / Sachs G / Suzuki H / Tani K / Fujiyoshi Y
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 /
Abstract: The gastric proton pump H,K-ATPase acidifies the gastric lumen, and thus its inhibitors, including the imidazo[1,2-a]pyridine class of K-competitive acid blockers (P-CABs), have potential application ...The gastric proton pump H,K-ATPase acidifies the gastric lumen, and thus its inhibitors, including the imidazo[1,2-a]pyridine class of K-competitive acid blockers (P-CABs), have potential application as acid-suppressing drugs. We determined the electron crystallographic structure of H,K-ATPase at 6.5 Å resolution in the E2P state with bound BYK99, a potent P-CAB with a restricted ring structure. The BYK99 bound structure has an almost identical profile to that of a previously determined structure with bound SCH28080, the original P-CAB prototype, but is significantly different from the previously reported P-CAB-free form, illustrating a common conformational change is required for P-CAB binding. The shared conformational changes include a distinct movement of transmembrane helix 2 (M2), from its position in the previously reported P-CAB-free form, to a location proximal to the P-CAB binding site in the present BYK99-bound structure. Site-specific mutagenesis within M2 revealed that D137 and N138, which face the P-CAB binding site in our model, significantly affect the inhibition constant (K ) of P-CABs. We also found that A335 is likely to be near the bridging nitrogen at the restricted ring structure of the BYK99 inhibitor. These provide clues to elucidate the binding site parameters and mechanism of P-CAB inhibition of gastric acid secretion.
History
DepositionJul 16, 2017-
Header (metadata) releaseAug 9, 2017-
Map releaseAug 9, 2017-
UpdateAug 9, 2017-
Current statusAug 9, 2017Processing site: PDBj / Status: Released

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Structure visualization

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

emd_6799.png

Downloads & links

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Map

FileDownload / File: emd_6799.map.gz / Format: CCP4 / Size: 15.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.004 / Movie #1: 0.004
Minimum - Maximum-0.01762751 - 0.02270848
Average (Standard dev.)-0.000006678895 (±0.003254603)
SymmetrySpace group: 18
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin-68-144-52
Dimensions137289105
Spacing136104288
CellA: 142.596 Å / B: 111.997604 Å / C: 319.9968 Å
α=β=γ: 90.0 °

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
Components
  • Complex: PIG GASTRIC H+/ K+ - ATPASE IN COMPLEX WITH BYK99
    • Protein or peptide: Potassium-transporting ATPase alpha chain 1
    • Protein or peptide: Potassium-transporting ATPase subunit beta

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Supramolecule #1: PIG GASTRIC H+/ K+ - ATPASE IN COMPLEX WITH BYK99

SupramoleculeName: PIG GASTRIC H+/ K+ - ATPASE IN COMPLEX WITH BYK99 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Sus scrofa (pig)

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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 / Number of copies: 1 / Enantiomer: LEVO / EC number: H+/K+-exchanging ATPase
Source (natural)Organism: Pig (pig) / Tissue: STOMACH
Molecular weightTheoretical: 114.399688 KDa
SequenceString: MGKAENYELY QVELGPGPSG DMAAKMSKKK AGRGGGKRKE KLENMKKEME INDHQLSVAE LEQKYQTSAT KGLSASLAAE LLLRDGPNA LRPPRGTPEY VKFARQLAGG LQCLMWVAAA ICLIAFAIQA SEGDLTTDDN LYLALALIAV VVVTGCFGYY Q EFKSTNII ...String:
MGKAENYELY QVELGPGPSG DMAAKMSKKK AGRGGGKRKE KLENMKKEME INDHQLSVAE LEQKYQTSAT KGLSASLAAE LLLRDGPNA LRPPRGTPEY VKFARQLAGG LQCLMWVAAA ICLIAFAIQA SEGDLTTDDN LYLALALIAV VVVTGCFGYY Q EFKSTNII ASFKNLVPQQ ATVIRDGDKF QINADQLVVG DLVEMKGGDR VPADIRILQA QGRKVDNSSL TGESEPQTRS PE CTHESPL ETRNIAFFST MCLEGTAQGL VVNTGDRTII GRIASLASGV ENEKTPIAIE IEHFVDIIAG LAILFGATFF IVA MCIGYT FLRAMVFFMA IVVAYVPEGL LATVTVCLSL TAKRLASKNC VVKNLEAVET LGSTSVICSD KTGTLTQNRM TVSH LWFDN HIHSADTTED QSGQTFDQSS ETWRALCRVL TLCNRAAFKS GQDAVPVPKR IVIGDASETA LLKFSELTLG NAMGY RERF PKVCEIPFNS TNKFQLSIHT LEDPRDPRHV LVMKGAPERV LERCSSILIK GQELPLDEQW REAFQTAYLS LGGLGE RVL GFCQLYLSEK DYPPGYAFDV EAMNFPTSGL SFAGLVSMID PPRATVPDAV LKCRTAGIRV IMVTGDHPIT AKAIAAS VG IISEGSETVE DIAARLRVPV DQVNRKDARA CVINGMQLKD MDPSELVEAL RTHPEMVFAR TSPQQKLVIV ESCQRLGA I VAVTGDGVND SPALKKADIG VAMGIAGSDA AKNAADMILL DDNFASIVTG VEQGRLIFDN LKKSIAYTLT KNIPELTPY LIYITVSVPL PLGCITILFI ELCTDIFPSV SLAYEKAESD IMHLRPRNPK RDRLVNEPLA AYSYFQIGAI QSFAGFTDYF TAMAQEGWF PLLCVGLRPQ WENHHLQDLQ DSYGQEWTFG QRLYQQYTCY TVFFISIEMC QIADVLIRKT RRLSAFQQGF F RNRILVIA IVFQVCIGCF LCYCPGMPNI FNFMPIRFQW WLVPMPFGLL IFVYDEIRKL GVRCCPGSWW DQELYY

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Macromolecule #2: Potassium-transporting ATPase subunit beta

MacromoleculeName: Potassium-transporting ATPase subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pig (pig) / Tissue: stomach
Molecular weightTheoretical: 33.113844 KDa
SequenceString: MAALQEKKSC SQRMEEFQRY CWNPDTGQML GRTLSRWVWI SLYYVAFYVV MSGIFALCIY VLMRTIDPYT PDYQDQLKSP GVTLRPDVY GEKGLDISYN VSDSTTWAGL AHTLHRFLAG YSPAAQEGSI NCTSEKYFFQ ESFLAPNHTK FSCKFTADML Q NCSGRPDP ...String:
MAALQEKKSC SQRMEEFQRY CWNPDTGQML GRTLSRWVWI SLYYVAFYVV MSGIFALCIY VLMRTIDPYT PDYQDQLKSP GVTLRPDVY GEKGLDISYN VSDSTTWAGL AHTLHRFLAG YSPAAQEGSI NCTSEKYFFQ ESFLAPNHTK FSCKFTADML Q NCSGRPDP TFGFAEGKPC FIIKMNRIVK FLPGNSTAPR VDCAFLDQPR DGPPLQVEYF PANGTYSLHY FPYYGKKAQP HY SNPLVAA KLLNVPRNRD VVIVCKILAE HVSFDNPHDP YEGKVEFKLK IQK

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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

Concentration6.5 mg/mL
BufferpH: 4.8
VitrificationCryogen name: NITROGEN / Instrument: LEICA KF80
DetailsThis sample is 2D crystal.

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Electron microscopy

MicroscopeJEOL KYOTO-3000SFF
Image recordingFilm or detector model: KODAK SO-163 FILM / Average electron dose: 8.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Camera length: 1500 mm

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.5 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Software - Name: MRC
Crystal parametersUnit cell - A: 142.6 Å / Unit cell - B: 112.0 Å / Unit cell - C: 320 Å / Unit cell - C sampling length: 320 Å / Unit cell - γ: 90 ° / Plane group: P 2 21 21
CTF correctionSoftware - Name: MRC
Crystallography statisticsNumber intensities measured: 59212 / Number structure factors: 4974 / Fourier space coverage: 47.1 / R sym: 0.469 / R merge: 0.469 / Overall phase error: 33.1 / Overall phase residual: 33.1 / Phase error rejection criteria: 0 / High resolution: 6.5 Å / Shell - Shell ID: 1 / Shell - High resolution: 6.5 Å / Shell - Low resolution: 200.0 Å / Shell - Number structure factors: 4974 / Shell - Phase residual: 33.1 / Shell - Fourier space coverage: 47.1 / Shell - Multiplicity: 11.9

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient
Output model

PDB-5y0b:
PIG GASTRIC H+,K+ - ATPASE IN COMPLEX with BYK99

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