23XO | pdb_000023xo

Cryo-EM structure of human sodium/proton antiporter NHE1 in complex with Rimeporide in an outward-open conformation

• PDB DOI: https://doi.org/10.2210/pdb23XO/pdb
• EM Map EMD-69360: EMDB EMDataResource

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


• Deposited: 2026-02-24 Released: 2026-04-08 
• Deposition Author(s): Cong, Y., Kong, F., Zhu, A., Yan, C.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.16 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure and transport mechanism of the human sodium/proton antiporter NHE1

Cong, Y., Kong, F., Zhu, A., Yan, C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 182.4 kDa 
• Atom Count: 6,636 
• Modeled Residue Count: 840 
• Deposited Residue Count: 1,630 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium/hydrogen exchanger 1	A, B	815	Homo sapiens	Mutation(s): 0  Gene Names: SLC9A1, APNH1, NHE1
UniProt & NIH Common Fund Data Resources
Find proteins for P19634 (Homo sapiens) Explore P19634  Go to UniProtKB:  P19634
PHAROS:  P19634 GTEx:  ENSG00000090020

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1E6E (Subject of Investigation/LOI)	C [auth A], D [auth B]	~{N}-carbamimidoyl-2-methyl-4,5-bis(methylsulfonyl)benzamide C11 H15 N3 O5 S2 GROMEQPXDKRRIE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.16 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.18_3855
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-04-08 
Deposition Author(s): Cong, Y., Kong, F., Zhu, A., Yan, C.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32171204

Revision History  

• Version 1.0: 2026-04-08
  Type: Initial release