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- EMDB-65385: cryo-EM structure of gastric proton pump bound to YK01 -

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Basic information

Entry
Database: EMDB / ID: EMD-65385
Titlecryo-EM structure of gastric proton pump bound to YK01
Map data
Sample
  • Complex: pig gastric proton pump alpha-beta complex
    • Protein or peptide: Sodium/potassium-transporting ATPase subunit alpha
    • Protein or peptide: Potassium-transporting ATPase subunit beta
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: MAGNESIUM ION
  • Ligand: YK01-b
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CHOLESTEROL
  • Ligand: water
KeywordsP-type ATPase / transporters / gastric / P-CABs / proton pump / MEMBRANE PROTEIN
Function / homology
Function and homology information


cation-transporting ATPase complex / potassium:proton exchanging ATPase complex / P-type potassium:proton transporter activity / Ion transport by P-type ATPases / sodium:potassium-exchanging ATPase complex / sodium ion export across plasma membrane / plasma membrane protein complex / intracellular sodium ion homeostasis / potassium ion import across plasma membrane / intracellular potassium ion homeostasis ...cation-transporting ATPase complex / potassium:proton exchanging ATPase complex / P-type potassium:proton transporter activity / Ion transport by P-type ATPases / sodium:potassium-exchanging ATPase complex / sodium ion export across plasma membrane / plasma membrane protein complex / intracellular sodium ion homeostasis / potassium ion import across plasma membrane / intracellular potassium ion homeostasis / 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
Similarity search - Function
Gastric H+/K+-transporter P-type ATPase, N-terminal / Gastric H+/K+-ATPase, N terminal domain / Sodium and potassium ATPases beta subunits signature 2. / 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. / : / 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 and potassium ATPases beta subunits signature 2. / 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. / : / 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 / P-type ATPase, cytoplasmic domain N / P-type ATPase actuator domain / 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
Sodium/potassium-transporting ATPase subunit alpha / Potassium-transporting ATPase subunit beta
Similarity search - Component
Biological speciesSus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.66 Å
AuthorsSaito H / Abe K
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24K01975 Japan
CitationJournal: Org Biomol Chem / Year: 2026
Title: Design, synthesis, and structural analysis of an inhibitor of the gastric proton pump with a diaza-tricyclic skeleton.
Authors: Nariyoshi Umekubo / Airi Hashizume / Haruki Saito / Satoru Kato / Chisato Kanai / Chai C Gopalasingam / Christoph Gerle / Hideki Shigematsu / Atsushi Yoshimori / Kazuhiro Abe / Satoshi Yokoshima /
Abstract: The development of potent K-competitive acid blockers (P-CABs) as inhibitors of acid gastric secretion attracts much research attention. In this study, the structure-guided design and ...The development of potent K-competitive acid blockers (P-CABs) as inhibitors of acid gastric secretion attracts much research attention. In this study, the structure-guided design and enantioselective synthesis of P-CABs yielded a diaza-tricyclic compound with moderate inhibitory activity against the gastric proton pump. The eutomer was experimentally confirmed, consistent with pharmacophore predictions, and its binding mode to the gastric proton pump was elucidated cryo-electron microscopy.
History
DepositionJul 16, 2025-
Header (metadata) releaseJan 14, 2026-
Map releaseJan 14, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65385.png

Downloads & links

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Map

FileDownload / File: emd_65385.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.752 Å
Density
Contour LevelBy AUTHOR: 0.163
Minimum - Maximum-1.0457981 - 1.462823
Average (Standard dev.)-0.0000028678232 (±0.024947591)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 338.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65385_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65385_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65385_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : pig gastric proton pump alpha-beta complex

EntireName: pig gastric proton pump alpha-beta complex
Components
  • Complex: pig gastric proton pump alpha-beta complex
    • Protein or peptide: Sodium/potassium-transporting ATPase subunit alpha
    • Protein or peptide: Potassium-transporting ATPase subunit beta
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: MAGNESIUM ION
  • Ligand: YK01-b
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CHOLESTEROL
  • Ligand: water

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Supramolecule #1: pig gastric proton pump alpha-beta complex

SupramoleculeName: pig gastric proton pump alpha-beta complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 130 KDa

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Macromolecule #1: Sodium/potassium-transporting ATPase subunit alpha

MacromoleculeName: Sodium/potassium-transporting ATPase subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 108.832141 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NDHQLSVAEL EQKYQTSATK GLSASLAAEL LLRDGPNALR PPRGTPEYVK FARQLAGGLQ CLMWVAAAIC LIAFAIQASE GDLTTDDNL YLALALIAVV VVTGCFGYYQ EFKSTNIIAS FKNLVPQQAT VIRDGDKFQI NADQLVVGDL VEMKGGDRVP A DIRILQAQ ...String:
NDHQLSVAEL EQKYQTSATK GLSASLAAEL LLRDGPNALR PPRGTPEYVK FARQLAGGLQ CLMWVAAAIC LIAFAIQASE GDLTTDDNL YLALALIAVV VVTGCFGYYQ EFKSTNIIAS FKNLVPQQAT VIRDGDKFQI NADQLVVGDL VEMKGGDRVP A DIRILQAQ GCKVDNSSLT GESEPQTRSP ECTHESPLET RNIAFFSTMC LEGTAQGLVV NTGDRTIIGR IASLASGVEN EK TPIAIEI EHFVDIIAGL AILFGATFFI VAMCIGYTFL RAMVFFMAIV VAYVPEGLLA TVTVCLSLTA KRLASKNCVV KNL EAVETL GSTSVICS(BFD)K TGTLTQNRMT VSHLWFDNHI HSADTTEDQS GQTFDQSSET WRALCRVLTL CNRAAFKSGQ DAVPVPKRI VIGDASETAL LKFSELTLGN AMGYRERFPK VCEIPFNSTN KFQLSIHTLE DPRDPRHVLV MKGAPERVLE R CSSILIKG QELPLDEQWR EAFQTAYLSL GGLGERVLGF CQLYLSEKDY PPGYAFDVEA MNFPTSGLCF AGLVSMIDPP RA TVPDAVL KCRTAGIRVI MVTGDHPITA KAIAASVGII SEGSETVEDI AARLRVPVDQ VNRKDARACV INGMQLKDMD PSE LVEALR THPEMVFART SPQQKLVIVE SCQRLGAIVA VTGDGVNDSP ALKKADIGVA MGIAGSDAAK NAADMILLDD NFAS IVTGV EQGRLIFDNL KKSIAYTLTK NIPELTPYLI YITVSVPLPL GCITILFIEL CTDIFPSVSL AYEKAESDIM HLRPR NPKR DRLVNEPLAA YSYFQIGAIQ SFAGFTDYFT AMAQEGWFPL LCVGLRPQWE NHHLQDLQDS YGQEWTFGQR LYQQYT CYT VFFISIEMCQ IADVLIRKTR RLSAFQQGFF RNRILVIAIV FQVCIGCFLC YCPGMPNIFN FMPIRFQWWL VPMPFSL LI FVYDEIRKLG VRCCPGSWWD QELYY

UniProtKB: Sodium/potassium-transporting ATPase subunit alpha

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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: Sus scrofa (pig)
Molecular weightTheoretical: 30.374691 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NPDTGQMLGR TLSRWVWISL YYVAFYVVMS GIFALCIYVL MRTIDPYTPD YQDQLKSPGV TLRPDVYGEK GLDISYNVSD STTWAGLAH TLHRFLAGYS PAAQEGSINC TSEKYFFQES FLAPNHTKFS CKFTADMLQN CSGRPDPTFG FAEGKPCFII K MNRIVKFL ...String:
NPDTGQMLGR TLSRWVWISL YYVAFYVVMS GIFALCIYVL MRTIDPYTPD YQDQLKSPGV TLRPDVYGEK GLDISYNVSD STTWAGLAH TLHRFLAGYS PAAQEGSINC TSEKYFFQES FLAPNHTKFS CKFTADMLQN CSGRPDPTFG FAEGKPCFII K MNRIVKFL PGNSTAPRVD CAFLDQPRDG PPLQVEYFPA NGTYSLHYFP YYGKKAQPHY SNPLVAAKLL NVPRNRDVVI VC KILAEHV SFDNPHDPYE GKVEFKLKIQ K

UniProtKB: Potassium-transporting ATPase subunit beta

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Macromolecule #3: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 3 / Number of copies: 5 / Formula: PCW
Molecular weightTheoretical: 787.121 Da
Chemical component information

ChemComp-PCW:
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DOPC, phospholipid*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: YK01-b

MacromoleculeName: YK01-b / type: ligand / ID: 5 / Number of copies: 1 / Formula: A1MA7
Molecular weightTheoretical: 347.496 Da

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #7: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 7 / Number of copies: 1 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 373 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 177544
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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