8PS0: Na/H antiporter NhaA

Cryo-EM structure of Sodium proton exchanger NhaA with bound cardiolipin. Determined by electron microscopy at 3.37 Å resolution. Released 21 Feb 2024.

Method: Electron microscopy
Resolution: 3.37 Å
Organism: Escherichia coli
Chains: 2
Atoms: 5,739
Mol. weight: 89 kDa
Ligands: CDL
Released: 21 Feb 2024

Explore 8PS0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8PS0 contains 41 α-helices and 10 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: 20 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	15-28	14
β-strand	31	1	1
β-strand	33	1	1
β-strand	45-50	6	2
β-strand	53-58	6	2
α-helix	59-84	26
α-helix	95-104	10
α-helix	107-112	6
α-helix	113-115	3
α-helix	120-123	4
α-helix	135-142	8
α-helix	150-173	24
α-helix	181-200	20
α-helix	205-218	14
α-helix	224-234	11
β-strand	242	1	3
β-strand	245	1	3
α-helix	247-258	12
α-helix	259-263	5
α-helix	287-294	8
α-helix	295-299	5
α-helix	300-311	12
α-helix	319-320	2
α-helix	325-334	10
α-helix	339-349	11
α-helix	355-378	24

Chain B: 21 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	16-30	15
α-helix	35-41	7
β-strand	45-49	5	2
β-strand	55-58	4	2
α-helix	59-85	27
α-helix	95-104	10
α-helix	107-116	10
α-helix	122-125	4
α-helix	135-143	9
α-helix	150-173	24
α-helix	181-200	20
α-helix	205-218	14
α-helix	223-236	14
β-strand	242	1	4
β-strand	245	1	4
α-helix	247-258	12
α-helix	259-263	5
α-helix	264-270	7
α-helix	281-284	4
α-helix	288-293	6
α-helix	294-299	6
α-helix	300-313	14
α-helix	326-335	10
α-helix	339-349	11
α-helix	355-379	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Na(+)/H(+) antiporter NhaA	A, B	protein	396	Escherichia coli	P13738 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8PS0_1 Na(+)/H(+) antiporter NhaA (chains A, B)
MKHLHRFFSSDASGGIILIIAAILAMIMANSGATSGWYHDFLETPVQLRVGSLEINKNML
LWINDALMAVFFLLVGLEVKRELMQGSLASLRQAAFPVIAAIGGMIVPTLLYLAFNYADP
ITREGWAIPAATDIAFALGVLALLGSRVPLALKIFLMALAIIDDLGAIIIIALFYTNDLS
MASLGVAAVAIAVLAVLNLCGARRTGVYILVGVVLWTAVLKSGVHATLAGVIVGFFIPLK
EKHGRSPAKRLEHVLHPWVAYLILPLFAFANAGVSLGGVTLDGLTSILPLGIIAGMLIGK
PLGISLFCWLALRLKLAHLPEGTTYQQIMVVGILCGIGFTMSIFIASLAFGSVDPELINW
AKLGILVGSISSAVIGYSWLRVRLRPSVGSENLYFQ

Ligands and cofactors

ID	Name	Formula	Copies
CDL	Cardiolipin	C81 H156 O17 P2	3

Primary citation

PIP 2 -mediated oligomerization of the endosomal sodium/proton exchanger NHE9. Kokane, S., Gulati, A., Meier, P.F. et al. Nat Commun (2025) 16:3055-3055. DOI 10.1038/s41467-025-58247-x · PubMed

Other PDB entries of the same protein (UniProt P13738 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7S24 2.2 Å, Crystal structure of the Na+/H+ antiporter NhaA at pH 6.5
9RH1 2.7 Å, Cryo-EM structure of the consensus inward-facing apo NhaA dimer at pH 7.5
9RH2 2.7 Å, Cryo-EM structure of the inward-facing apo NhaA in the unplugged state at pH 7.5
9RH3 2.7 Å, Cryo-EM structure of the inward-facing apo NhaA in the plugged state at pH 7.5
9RHB 2.9 Å, Cryo-EM structure of the inward-facing apo NhaA in the open-funnel state at pH 8.5
9RHF 3.0 Å, Cryo-EM structure of the inward-facing sodium-bound NhaA at pH 8.5
9RH4 3.1 Å, Cryo-EM structure of the inward-facing apo NhaA with flexible N-terminus at pH 7.5
9RH8 3.1 Å, Cryo-EM structure of the inward-facing apo NhaA in the unplugged state at pH 5.5
9RH9 3.1 Å, Cryo-EM structure of the inward-facing apo NhaA in the plugged state at pH 5.5
9RHC 3.2 Å, Cryo-EM structure of the inward-facing apo NhaA in the unplugged state at pH 8.5
9RHD 3.2 Å, Cryo-EM structure of the inward-facing apo NhaA in the plugged state at pH 8.5
9RH5 3.3 Å, Cryo-EM structure of the inward-facing apo NhaA in the unplugged state at pH 6.3

Browse structure collections

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