9KCM | pdb_00009kcm

Cryo-EM structure of human sodium pump E1003K complexed with NDRG3 and TMX2 in (2Na+)E1-AMPPCP state

• PDB DOI: https://doi.org/10.2210/pdb9KCM/pdb
• EM Map EMD-62256: 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., Matsui, R., 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 

Literature

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

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 207.86 kDa 
• Atom Count: 12,419 
• Modeled Residue Count: 1,580 
• Deposited Residue Count: 1,858 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium/potassium-transporting ATPase subunit beta-3	A [auth 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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein NDRG3	B [auth N]	298	Homo sapiens	Mutation(s): 0  Gene Names: NDRG3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UGV2 (Homo sapiens) Explore Q9UGV2  Go to UniProtKB:  Q9UGV2
PHAROS:  Q9UGV2 GTEx:  ENSG00000101079

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium/potassium-transporting ATPase subunit alpha-1	C [auth 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 ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin-related transmembrane protein 2	D [auth T]	296	Homo sapiens	Mutation(s): 0  Gene Names: TMX2, TXNDC14, CGI-31, My009, PIG26, PSEC0045, UNQ237/PRO270
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y320 (Homo sapiens) Explore Q9Y320  Go to UniProtKB:  Q9Y320
PHAROS:  Q9Y320 GTEx:  ENSG00000213593

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACP (Subject of Investigation/LOI)	E [auth A]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C11 H18 N5 O12 P3 UFZTZBNSLXELAL-IOSLPCCCSA-N
NA (Subject of Investigation/LOI)	F [auth A], G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-12 
Deposition Author(s): Abe, K., Matsui, R., Dou, Y., Suzuki, J.

---

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	21H02426

Revision History  

• Version 1.0: 2025-11-12
  Type: Initial release