9KCG | pdb_00009kcg

Cryo-EM structure of human sodium pump WT in (3Na+)E1-AMPPCP state

PDB DOI: https://doi.org/10.2210/pdb9KCG/pdb
EM Map EMD-62250: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

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: 3.10 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: 164.73 kDa
Atom Count: 10,349
Modeled Residue Count: 1,283
Deposited Residue Count: 1,442
Unique protein chains: 3

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): 0 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

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
FXYD domain-containing ion transport regulator 5	C	178	Homo sapiens	Mutation(s): 0 Gene Names: FXYD5, DYSAD, IWU1, HSPC113, UNQ2561/PRO6241
UniProt & NIH Common Fund Data Resources
Find proteins for Q96DB9 (Homo sapiens) Explore Q96DB9 Go to UniProtKB: Q96DB9
PHAROS: Q96DB9 GTEx: ENSG00000089327
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96DB9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PC1 Query on PC1 Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain J [auth A]	J [auth A], N [auth B]	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₈ N O₈ P NRJAVPSFFCBXDT-HUESYALOSA-N		Interactions Focus chain J [auth A] Focus chain N [auth B] Interactions & Density Focus chain J [auth A] Focus chain N [auth B]
PCW Query on PCW Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain L [auth A] MOL2 format, chain M [auth B] MOL2 format, chain L [auth A] mmCIF format, chain M [auth B] mmCIF format, chain L [auth A]	L [auth A], M [auth B]	1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₅ N O₈ P SNKAWJBJQDLSFF-NVKMUCNASA-O		Interactions Focus chain L [auth A] Focus chain M [auth B] Interactions & Density Focus chain L [auth A] Focus chain M [auth B]
ACP (Subject of Investigation/LOI) Query on ACP Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ UFZTZBNSLXELAL-IOSLPCCCSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
CLR Query on CLR Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain K [auth A] SDF format, chain H [auth A] MOL2 format, chain O [auth B] MOL2 format, chain K [auth A] MOL2 format, chain H [auth A] mmCIF format, chain O [auth B] mmCIF format, chain K [auth A] mmCIF format, chain H [auth A]	H [auth A], K [auth A], O [auth B]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain H [auth A] Focus chain K [auth A] Focus chain O [auth B] Interactions & Density Focus chain H [auth A] Focus chain K [auth A] Focus chain O [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
NA (Subject of Investigation/LOI) Query on NA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]