23XI: Human sodium/proton antiporter NHE1

Cryo-EM structure of human sodium/proton antiporter NHE1 in complex with Zoniporide in an outward-open conformation. Determined by electron microscopy at 2.93 Å resolution. Released 5 Aug 2026.

Method: Electron microscopy
Resolution: 2.93 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,749
Mol. weight: 184.12 kDa
Ligands: A1E6C, PS1
Released: 5 Aug 2026

Explore 23XI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

23XI contains 47 α-helices and 4 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 24 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	100-121	22
α-helix	124-128	5
α-helix	131-149	19
α-helix	158-160	3
α-helix	161-165	5
α-helix	166-175	10
α-helix	179-184	6
α-helix	186-190	5
α-helix	191-196	6
α-helix	197-213	17
α-helix	224-234	11
β-strand	237	1	1
α-helix	239-246	8
α-helix	253-264	12
α-helix	267-282	16
α-helix	288-321	34
α-helix	330-347	18
α-helix	352-369	18
α-helix	376-403	28
α-helix	411-437	27
α-helix	446-453	8
β-strand	458	1	1
α-helix	460-467	8
α-helix	477-489	13
α-helix	490-495	6
α-helix	496-505	10

Chain B: 23 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	100-121	22
α-helix	124-128	5
α-helix	131-149	19
α-helix	158-160	3
α-helix	161-165	5
α-helix	166-175	10
α-helix	179-184	6
α-helix	186-190	5
α-helix	191-196	6
α-helix	197-213	17
α-helix	224-234	11
β-strand	237	1	2
α-helix	239-246	8
α-helix	253-282	30
α-helix	288-321	34
α-helix	330-347	18
α-helix	352-369	18
α-helix	376-403	28
α-helix	411-437	27
α-helix	446-453	8
β-strand	458	1	2
α-helix	460-467	8
α-helix	477-489	13
α-helix	490-495	6
α-helix	496-505	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sodium/hydrogen exchanger 1	A, B	protein	815	Homo sapiens	P19634 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>23XI_1 Sodium/hydrogen exchanger 1 (chains A, B)
MVLRSGICGLSPHRIFPSLLVVVALVGLLPVLRSHGLQLSPTASTIRSSEPPRERSIGDV
TTAPPEVTPESRPVNHSVTDHGMKPRKAFPVLGIDYTHVRTPFEISLWILLACLMKIGFH
VIPTISSIVPESCLLIVVGLLVGGLIKGVGETPPFLQSDVFFLFLLPPIILDAGYFLPLR
QFTENLGTILIFAVVGTLWNAFFLGGLMYAVCLVGGEQINNIGLLDNLLFGSIISAVDPV
AVLAVFEEIHINELLHILVFGESLLNDAVTVVLYHLFEEFANYEHVGIVDIFLGFLSFFV
VALGGVLVGVVYGVIAAFTSRFTSHIRVIEPLFVFLYSYMAYLSAELFHLSGIMALIASG
VVMRPYVEANISHKSHTTIKYFLKMWSSVSETLIFIFLGVSTVAGSHHWNWTFVISTLLF
CLIARVLGVLGLTWFINKFRIVKLTPKDQFIIAYGGLRGAIAFSLGYLLDKKHFPMCDLF
LTAIITVIFFTVFVQGMTIRPLVDLLAVKKKQETKRSINEEIHTQFLDHLLTGIEDICGH
YGHHHWKDKLNRFNKKYVKKCLIAGERSKEPQLIAFYHKMEMKQAIELVESGGMGKIPSA
VSTVSMQNIHPKSLPSERILPALSKDKEEEIRKILRNNLQKTRQRLRSYNRHTLVADPYE
EAWNQMLLRRQKARQLEQKINNYLTVPAHKLDSPTMSRARIGSDPLAYEPKEDLPVITID
PASPQSPESVDLVNEELKGKVLGLSRDPAKVAEEDEDDDGGIMMRSKETSSPGTDDVFTP
APSDSPSSQRIQRCLSDPGPHPEPGEGEPFFPKGQ

Ligands and cofactors

ID	Name	Formula	Copies
A1E6C	Zoniporide	C17 H16 N6 O	2
PS1	1,2-didecanoyl-sn-glycero-3-[phospho-L-serine]	C26 H49 N O10 P	3

Water and common crystallization additives (NA) are not listed.

Primary citation

Structure and transport mechanism of the human sodium/proton antiporter NHE1. Cong, Y., Kong, F., Zhu, A. et al. To be published.

Other PDB entries of the same protein (UniProt P19634 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6NUC 1.9 Å, Structure of Calcineurin in complex with NHE1 peptide
6NUF 1.9 Å, Structure of Calcineurin in complex with NHE1 peptide
9NXE 2.09 Å, Crystal Structure of Calcineurin Clinical Variant E282K
2YGG 2.23 Å, Complex of CaMBR and CaM
6NUU 2.3 Å, Structure of Calcineurin mutant in complex with NHE1 peptide
2BEC 2.7 Å, Crystal structure of CHP2 in complex with its binding region in NHE1 and insights into…
23XK 3.1 Å, Cryo-EM structure of human sodium/proton antiporter NHE1 in complex with Cariporide in…
23XO 3.16 Å, Cryo-EM structure of human sodium/proton antiporter NHE1 in complex with Rimeporide in…
23XM 3.24 Å, Cryo-EM structure of human sodium/proton antiporter NHE1 in complex with Eniporide in an…
7DSW 3.3 Å, Structure of a human NHE1-CHP1 complex under pH 7.5
7DSV 3.4 Å, Structure of a human NHE1-CHP1 complex under pH 6.5
7DSX 3.5 Å, Structure of a human NHE1-CHP1 complex under pH 7.5, bound by cariporide

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