9KCK | pdb_00009kck

Cryo-EM structure of human sodium pump E1003K in (2K+)E2-AlF state

PDB DOI: https://doi.org/10.2210/pdb9KCK/pdb
EM Map EMD-62254: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2024-11-01 Released: 2025-11-12
Deposition Author(s): Abe, K., Dou, Y., Suzuki, J.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural basis of a sodium pump quaternary complex leading phospholipid scrambling in the living cell

Dou, Y., Abe, K., Suzuki, J.

To be published.

Macromolecule Content

Total Structure Weight: 140.96 kDa
Atom Count: 9,800
Modeled Residue Count: 1,252
Deposited Residue Count: 1,264
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-1	A	985	Homo sapiens	Mutation(s): 1 Gene Names: ATP1A1 EC: 7.2.2.13
UniProt & NIH Common Fund Data Resources
Find proteins for P05023 (Homo sapiens) Explore P05023 Go to UniProtKB: P05023
PHAROS: P05023 GTEx: ENSG00000163399
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05023
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium/potassium-transporting ATPase subunit beta-3	B	279	Homo sapiens	Mutation(s): 0 Gene Names: ATP1B3
UniProt & NIH Common Fund Data Resources
Find proteins for P54709 (Homo sapiens) Explore P54709 Go to UniProtKB: P54709
PHAROS: P54709 GTEx: ENSG00000069849
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P54709
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CLR Query on CLR Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
ALF Query on ALF 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]	TETRAFLUOROALUMINATE ION Al F₄ UYOMQIYKOOHAMK-UHFFFAOYSA-J		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
K (Subject of Investigation/LOI) Query on K Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]