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

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Basic information

Entry
Database: PDB / ID: 5y0b
TitlePIG GASTRIC H+,K+ - ATPASE IN COMPLEX with BYK99
Components
  • Potassium-transporting ATPase alpha chain 1
  • Potassium-transporting ATPase subunit beta
KeywordsHYDROLASE / ion pump / h+ / k+-atpase / p-type atpase / membrane protein / e2 / aluminium fluoride / ATP-binding / hydrogen ion transport / ion transport / magnesium / membrane / metal-binding / nucleotide-binding / phosphoprotein / potassium / potassium transport / transmembrane / transport / disulfide bond / glycoprotein / signal-anchor
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 / haloacid dehalogenase-like hydrolase ...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 / haloacid dehalogenase-like hydrolase / 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)
MethodELECTRON CRYSTALLOGRAPHY / electron 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.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan
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, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release

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Assembly

Deposited unit
A: Potassium-transporting ATPase alpha chain 1
B: Potassium-transporting ATPase subunit beta


Theoretical massNumber of molelcules
Total (without water)147,5142
Polymers147,5142
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-24 kcal/mol
Surface area54910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.600, 112.000, 320.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Potassium-transporting ATPase alpha chain 1 / Gastric H+/K+ ATPase subunit alpha / Proton pump


Mass: 114399.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Tissue: STOMACH / References: UniProt: P19156, H+/K+-exchanging ATPase
#2: Protein Potassium-transporting ATPase subunit beta / Gastric H+/K+ ATPase subunit beta / Proton pump beta chain / gp60-90


Mass: 33113.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Tissue: stomach / References: UniProt: P18434

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: electron crystallography
Crystal symmetry∠γ: 90 ° / C sampling length: 320 Å / A: 142.6 Å / B: 112 Å / C: 320 Å / Space group name H-M: P22121

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Sample preparation

ComponentName: PIG GASTRIC H+/ K+ - ATPASE IN COMPLEX WITH BYK99 / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Sus scrofa (pig) / Tissue: stomach
Buffer solutionpH: 4.8
SpecimenConc.: 6.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample is 2D crystal.
VitrificationInstrument: LEICA KF80 / Cryogen name: NITROGEN
Crystal growpH: 4.87

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Data collection

MicroscopyModel: JEOL KYOTO-3000SFF
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 8 e/Å2 / Film or detector model: KODAK SO-163 FILM
EM diffractionCamera length: 1500 mm
EM diffraction shellResolution: 6.5→200 Å / Fourier space coverage: 47.1 % / Multiplicity: 11.9 / Num. of structure factors: 4974 / Phase residual: 33.1 °
EM diffraction statsFourier space coverage: 47.1 % / High resolution: 6.5 Å / Num. of intensities measured: 59212 / Num. of structure factors: 4974 / Phase error: 33.1 ° / Phase residual: 33.1 ° / Phase error rejection criteria: 0 / Rmerge: 0.469 / Rsym: 0.469

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Processing

EM software
IDNameCategory
1MRCimage acquisition
3MRCCTF correction
6SITUSmodel fitting
12MRC3D reconstruction
13COOTmodel refinement
Crystal symmetry∠γ: 90 ° / C sampling length: 320 Å / A: 142.6 Å / B: 112 Å / C: 320 Å / Space group name H-M: P22121
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 6.5 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 2D CRYSTAL
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: correlation coefficient
RefinementResolution: 6.7→200 Å / Cross valid method: THROUGHOUT /
Num. reflection% reflection
obs4974 50.1 %
Refinement stepCycle: 1 /
ProteinNucleic acidLigandSolvent
Num. atoms1044 0 0 0

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