9RH1: Consensus inward-facing apo NhaA dimer at pH 7.5

Cryo-EM structure of the consensus inward-facing apo NhaA dimer at pH 7.5. Determined by electron microscopy at 2.7 Å resolution. Released 17 Jun 2026.

Method: Electron microscopy
Resolution: 2.7 Å
Organisms: Escherichia coli, Mus musculus
Chains: 6
Atoms: 9,218
Mol. weight: 143.64 kDa
Ligands: CDL, PGT
Released: 17 Jun 2026

Explore 9RH1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9RH1 contains 56 α-helices and 56 β-strands across 6 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.

Chains A and D: 23 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	13-30	18
α-helix	32-42	11
β-strand	45-50	6	1
β-strand	53-58	6	1
α-helix	59-84	26
α-helix	91-116	26
α-helix	122-125	4
α-helix	128-130	3
α-helix	134-142	9
α-helix	145-147	3
α-helix	150-174	25
α-helix	181-199	19
α-helix	205-218	14
α-helix	223-236	14
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	325-334	10
α-helix	339-350	12
α-helix	355-383	29
α-helix	385-386	2

Chains B and E: 2 helices, 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
α-helix	100	1
β-strand	105-108	4	4
β-strand	112-116	5	4

Chain C: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	5
β-strand	10-12	3	6
β-strand	19-20	2	5
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	62-66	5	5
β-strand	70-75	6	5
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

Chain F: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	10
β-strand	10-12	3	11
β-strand	19-20	2	10
β-strand	23-25	3	10
β-strand	33-38	6	11
β-strand	44-49	6	11
β-strand	53-54	2	11
α-helix	55	1
β-strand	62-66	5	10
β-strand	70-75	6	10
α-helix	80-82	3
β-strand	85-90	6	11
α-helix	96	1
β-strand	97-98	2	11
β-strand	102-105	4	11

Molecules and chains

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

Sequence of entity 1 (A, D), FASTA

>9RH1_1 Na(+)/H(+) antiporter NhaA (chains A, D)
MKHLHRFFSSDASGGIILIIAAILAMIMANSGATSGWYHDFLETPVQLRVGSLEINKNML
LWINDALMAVFFLLVGLEVKRELMQGSLASLRQAAFPVIAAIGGMIVPALLYLAFNYADP
ITREGWAIPAATDIAFALGVLALLGSRVPLALKIFLMALAIIDDLGAIIIIALFYTNDLS
MASLGVAAVAIAVLAVLNLCGARRTGVYILVGVVLWTAVLKSGVHATLAGVIVGFFIPLK
EKHGRSPAKRLEHVLHPWVAYLILPLFAFANAGVSLQGVTLDGLTSILPLGIIAGLLIGK
PLGISLFCWLALRLKLAHLPEGTTYQQIMVVGILCGIGFTMSIFIASLAFGSVDPELINW
AKLGILVGSISSAVIGYSWLRVRLRPSVAAAIEGRIEGRLEHHHHHH

Sequence of entity 2 (B, E), FASTA

>9RH1_2 Fv6F9 heavy chain (chains B, E)
EVKLHQSGAELVRPGASVKLSCKALGYTFSDYEMHWVKQTPVHGLEWIGAIHPGSGGTAY
NQKFKGKATLTADKSSSTAYMELSSLTSEDPAVYYCTKEEYGNDFDYWGQGTTVTVSSAW
RHPQFGG

Sequence of entity 3 (C, F), FASTA

>9RH1_3 Fv6F9 light chain (chains C, F)
DIELTQTPSSLSASLGERVSLTCRASQEISGYLSWLQQKPDGTIKRLIYAASTLDSGVPK
RFSGSRSGSDYSLTISSLESEDFADYYCLQYASYPFTFGSGTKLEIKREQKLISEEDLN

Ligands and cofactors

ID	Name	Formula	Copies
CDL	Cardiolipin	C81 H156 O17 P2	1
PGT	(1S)-2-{[{[(2R)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoylo…	C40 H79 O10 P	1

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
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
8PS0 3.37 Å, Cryo-EM structure of Sodium proton exchanger NhaA with bound cardiolipin

Browse structure collections

About this viewer

MolViewer shows 9RH1 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.