5YLV | pdb_00005ylv

Crystal structure of the gastric proton pump complexed with SCH28080

• PDB DOI: https://doi.org/10.2210/pdb5YLV/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Sus scrofa
• Expression System: Homo sapiens
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2017-10-19 Released: 2018-04-11 
• Deposition Author(s): Abe, K., Irie, K., Nakanishi, H., Fujiyoshi, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.292 (Depositor), 0.293 (DCC) 
• R-Value Work: 
  0.240 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.242 (Depositor) 

Starting Model: experimental

Literature

Crystal structures of the gastric proton pump

Abe, K., Irie, K., Nakanishi, H., Suzuki, H., Fujiyoshi, Y.

(2018) Nature 556: 214-218

• PubMed: 29618813 
• DOI: https://doi.org/10.1038/s41586-018-0003-8
• Primary Citation Related Structures: 
  5YLU, 5YLV


• PubMed Abstract: 
  

  The gastric proton pump-the H ⁺ , K ⁺ -ATPase-is a P-type ATPase responsible for acidifying the gastric juice down to pH 1. This corresponds to a million-fold proton gradient across the membrane of the parietal cell, the steepest known cation gradient of any mammalian tissue. The H ⁺ , K ⁺ -ATPase is an important target for drugs that treat gastric acid-related diseases. Here we present crystal structures of the H ⁺ , K ⁺ -ATPase in complex with two blockers, vonoprazan and SCH28080, in the luminal-open state, at 2.8 Å resolution. The drugs have partially overlapping but clearly distinct binding modes in the middle of a conduit running from the gastric lumen to the cation-binding site. The crystal structures suggest that the tight configuration at the cation-binding site lowers the pK _a value of Glu820 sufficiently to enable the release of a proton even into the pH 1 environment of the stomach.

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Organizational Affiliation: 
• Cellular and Structural Physiology Institute, Nagoya University, Nagoya, Japan. [e-mail].
Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan. [e-mail].
Japan Core Research for Evolutional Science and Technology, Japan Science and Technology Corporation, Nagoya, Japan. [e-mail].
Cellular and Structural Physiology Institute, Nagoya University, Nagoya, Japan.
Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan.
Japan Core Research for Evolutional Science and Technology, Japan Science and Technology Corporation, Nagoya, Japan.
Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, NY, USA.
CeSPIA Inc., Tokyo, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 150.53 kDa 
• Atom Count: 9,937 
• Modeled Residue Count: 1,248 
• Deposited Residue Count: 1,323 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Potassium-transporting ATPase alpha chain 1	A	1,034	Sus scrofa	Mutation(s): 3  Gene Names: ATP4A EC: 3.6.3.10 (PDB Primary Data), 7.2.2.19 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P19156 (Sus scrofa) Explore P19156  Go to UniProtKB:  P19156

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Potassium-transporting ATPase subunit beta	B	289	Sus scrofa	Mutation(s): 0  Gene Names: ATP4B Membrane Entity: Yes
UniProt
Find proteins for P18434 (Sus scrofa) Explore P18434  Go to UniProtKB:  P18434
Glycosylation
Glycosylation Sites: 3

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PCW	L [auth B]	1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C44 H85 N O8 P SNKAWJBJQDLSFF-NVKMUCNASA-O
CE1	E [auth A], M [auth B]	O-DODECANYL OCTAETHYLENE GLYCOL C28 H58 O9 YYELLDKEOUKVIQ-UHFFFAOYSA-N
8WX	C [auth A]	2-(2-methyl-8-phenylmethoxy-imidazo[1,2-a]pyridin-3-yl)ethanenitrile C17 H15 N3 O PYKJFEPAUKAXNN-UHFFFAOYSA-N
NAG	I [auth B], J [auth B], K [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
RB	F [auth A], G [auth A], H [auth A]	RUBIDIUM ION Rb NCCSSGKUIKYAJD-UHFFFAOYSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
BFD	A	L-PEPTIDE LINKING	C4 H6 Be F3 N O4		ASP

Binding Affinity Annotations
ID	Source	Binding Affinity
8WX	BindingDB:  5YLV	IC50: min: 65, max: 1590 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.292 (Depositor), 0.293 (DCC) 
• R-Value Work:  0.240 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.242 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.05	α = 90
b = 105.05	β = 90
c = 368.54	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-04-11 
Deposition Author(s): Abe, K., Irie, K., Nakanishi, H., Fujiyoshi, Y.

Revision History  

• Version 1.0: 2018-04-11
  Type: Initial release
  
• Version 1.1: 2018-04-18
  Changes: Data collection, Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2023-11-22
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.4: 2024-11-20
  Changes: Structure summary