9RHF: Inward-facing sodium-bound NhaA at pH 8.5

Cryo-EM structure of the inward-facing sodium-bound NhaA at pH 8.5. Determined by electron microscopy at 3.0 Å resolution. Released 17 Jun 2026.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Escherichia coli, Mus musculus
Chains: 3
Atoms: 4,643
Mol. weight: 70.74 kDa
Released: 17 Jun 2026

Explore 9RHF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9RHF contains 32 α-helices and 29 β-strands across 3 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: 28 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	2-9	8
α-helix	12-30	19
α-helix	35-42	8
β-strand	45-50	6	1
β-strand	53-58	6	1
α-helix	59-62	4
α-helix	63-67	5
α-helix	68-84	17
α-helix	86-88	3
α-helix	91-116	26
α-helix	120-123	4
α-helix	128-130	3
α-helix	134-144	11
α-helix	145-147	3
α-helix	150-174	25
α-helix	181-199	19
α-helix	205-221	17
α-helix	228-236	9
β-strand	242	1	2
β-strand	245	1	2
α-helix	247-258	12
α-helix	259-263	5
α-helix	264-271	8
α-helix	283-285	3
α-helix	287-293	7
α-helix	294-299	6
α-helix	300-313	14
α-helix	319-320	2
α-helix	325-334	10
α-helix	340-350	11
α-helix	355-381	27
α-helix	385-386	2

Chain B: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	3
β-strand	10-12	3	4
β-strand	18-25	8	3
α-helix	29-31	3
β-strand	34-40	7	4
β-strand	44-51	8	4
β-strand	58-60	3	4
β-strand	65	1	3
β-strand	68-73	6	3
β-strand	78-83	6	3
β-strand	92-99	8	4
β-strand	105-108	4	4
β-strand	112-116	5	4

Chain C: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	5
β-strand	10-12	3	6
β-strand	19-20	2	7
β-strand	23-25	3	5
β-strand	33-38	6	6
β-strand	44-49	6	6
β-strand	53-54	2	6
α-helix	55	1
β-strand	64-67	4	5
β-strand	70-73	4	5
β-strand	74-75	2	7
α-helix	80-82	3
β-strand	85-90	6	6
α-helix	96	1
β-strand	97-98	2	6
β-strand	102-105	4	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Na(+)/H(+) antiporter NhaA	A	protein	407	Escherichia coli	P13738 (AlphaFold model)
Fv6F9 heavy chain	B	protein	127	Mus musculus
Fv6F9 light chain	C	protein	119	Mus musculus

Sequence of entity 1 (A), FASTA

>9RHF_1 Na(+)/H(+) antiporter NhaA (chains A)
MKHLHRFFSSDASGGIILIIAAILAMIMANSGATSGWYHDFLETPVQLRVGSLEINKNML
LWINDALMAVFFLLVGLEVKRELMQGSLASLRQAAFPVIAAIGGMIVPALLYLAFNYADP
ITREGWAIPAATDIAFALGVLALLGSRVPLALKIFLMALAIIDDLGAIIIIALFYTNDLS
MASLGVAAVAIAVLAVLNLCGARRTGVYILVGVVLWTAVLKSGVHATLAGVIVGFFIPLK
EKHGRSPAKRLEHVLHPWVAYLILPLFAFANAGVSLQGVTLDGLTSILPLGIIAGLLIGK
PLGISLFCWLALRLKLAHLPEGTTYQQIMVVGILCGIGFTMSIFIASLAFGSVDPELINW
AKLGILVGSISSAVIGYSWLRVRLRPSVAAAIEGRIEGRLEHHHHHH

Sequence of entity 2 (B), FASTA

>9RHF_2 Fv6F9 heavy chain (chains B)
EVKLHQSGAELVRPGASVKLSCKALGYTFSDYEMHWVKQTPVHGLEWIGAIHPGSGGTAY
NQKFKGKATLTADKSSSTAYMELSSLTSEDPAVYYCTKEEYGNDFDYWGQGTTVTVSSAW
RHPQFGG

Sequence of entity 3 (C), FASTA

>9RHF_3 Fv6F9 light chain (chains C)
DIELTQTPSSLSASLGERVSLTCRASQEISGYLSWLQQKPDGTIKRLIYAASTLDSGVPK
RFSGSRSGSDYSLTISSLESEDFADYYCLQYASYPFTFGSGTKLEIKREQKLISEEDLN

Primary citation

pH-dependent activation of the Na + /H + antiporter NhaA and conformational dynamics of its N-terminus. Weng, T.H., Fabian, B., Olkhova, E. et al. Nat Commun (2026) 17. DOI 10.1038/s41467-026-73424-2 · 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
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
8PS0 3.37 Å, Cryo-EM structure of Sodium proton exchanger NhaA with bound cardiolipin

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