7EFN | pdb_00007efn

Crystal structure of the gastric proton pump K791S/E820D/Y340N/E936V in (BYK)E2BeF state

PDB DOI: https://doi.org/10.2210/pdb7EFN/pdb

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

Deposited: 2021-03-22 Released: 2021-09-01
Deposition Author(s): Abe, K., Yamamoto, K., Irie, K.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.308 (Depositor), 0.312 (DCC)
R-Value Work:
0.268 (Depositor), 0.269 (DCC)
R-Value Observed:
0.270 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Gastric proton pump with two occluded K + engineered with sodium pump-mimetic mutations.

Abe, K., Yamamoto, K., Irie, K., Nishizawa, T., Oshima, A.

(2021) Nat Commun 12: 5709-5709

PubMed: 34588453 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-021-26024-1
Primary Citation Related Structures:
7EFL, 7EFM, 7EFN, 7ET1

PubMed Abstract:
The gastric H ⁺,K ⁺-ATPase mediates electroneutral exchange of 1H ⁺/1K ⁺ per ATP hydrolysed across the membrane. Previous structural analysis of the K ⁺-occluded E2-P transition state of H ⁺,K ⁺-ATPase showed a single bound K ⁺ at cation-binding site II, in marked contrast to the two K ⁺ ions occluded at sites I and II of the closely-related Na ⁺,K ⁺-ATPase which mediates electrogenic 3Na ⁺/2K ⁺ translocation across the membrane. The molecular basis of the different K ⁺ stoichiometry between these K ⁺-counter-transporting pumps is elusive. We show a series of crystal structures and a cryo-EM structure of H ⁺,K ⁺-ATPase mutants with changes in the vicinity of site I, based on the structure of the sodium pump. Our step-wise and tailored construction of the mutants finally gave a two-K ⁺ bound H ⁺,K ⁺-ATPase, achieved by five mutations, including amino acids directly coordinating K ⁺ (Lys791Ser, Glu820Asp), indirectly contributing to cation-binding site formation (Tyr340Asn, Glu936Val), and allosterically stabilizing K ⁺-occluded conformation (Tyr799Trp). This quintuple mutant in the K ⁺-occluded E2-P state unambiguously shows two separate densities at the cation-binding site in its 2.6 Å resolution cryo-EM structure. These results offer new insights into how two closely-related cation pumps specify the number of K ⁺ accommodated at their cation-binding site.

Organizational Affiliation

Cellular and Structural Physiology Institute, Nagoya University, Nagoya, 464-8601, Japan. kabe@cespi.nagoya-u.ac.jp.

Macromolecule Content

Total Structure Weight: 139.91 kDa
Atom Count: 9,845
Modeled Residue Count: 1,246
Deposited Residue Count: 1,246
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium/potassium-transporting ATPase subunit alpha	A	985	Sus scrofa	Mutation(s): 4 Gene Names: ATP4A EC: 7.2.2.19 Membrane Entity: Yes
UniProt
Find proteins for P19156 (Sus scrofa) Explore P19156 Go to UniProtKB: P19156
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P19156
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Potassium-transporting ATPase subunit beta	B	261	Sus scrofa	Mutation(s): 0 Gene Names: ATP4B Membrane Entity: Yes
UniProt
Find proteins for P18434 (Sus scrofa) Explore P18434 Go to UniProtKB: P18434
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P18434
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain B
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
J3C (Subject of Investigation/LOI) Query on J3C Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	(7R,8R,9S)-2,3-dimethyl-9-phenyl-7,8,9,10-tetrahydroimidazo[1,2-h][1,7]naphthyridine-7,8-diol C₁₈ H₁₉ N₃ O₂ FHHGNULEXOWEKU-USXIJHARSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	I [auth B], J [auth B], K [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]
RB Query on RB Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	D [auth A], E [auth A], G [auth A], H [auth A]	RUBIDIUM ION Rb NCCSSGKUIKYAJD-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]