9H2P: Low conductance mechanosensitive channel YnaI

YnaI in its open conformation purified in DDM showing ligand-filled pockets. Determined by electron microscopy at 2.3 Å resolution. Released 24 Sept 2025.

Method: Electron microscopy
Resolution: 2.3 Å
Organism: Escherichia coli
Chains: 7
Atoms: 18,984
Mol. weight: 269.33 kDa
Ligands: D12
Released: 24 Sept 2025

Explore 9H2P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9H2P contains 84 α-helices and 84 β-strands across 7 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, B, C, D, E, F and G: 12 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	8-29	22
α-helix	42-68	27
α-helix	77-108	32
α-helix	112-133	22
α-helix	143-146	4
α-helix	151-176	26
β-strand	184-185	2	1
β-strand	186	1	2
β-strand	194-199	6	1
β-strand	203-207	5	1
β-strand	213-217	5	1
α-helix	218-221	4
β-strand	226-227	2	2
α-helix	229-231	3
β-strand	235-243	9	3
α-helix	245-250	6
α-helix	251-263	13
β-strand	268	1	3
β-strand	275-281	7	3
β-strand	286-294	9	3
α-helix	299-319	21
β-strand	324	1	3
α-helix	325-326	2
β-strand	328-333	6	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Low conductance mechanosensitive channel YnaI	A, B, C, D, E, F, G	protein	332	Escherichia coli	P0AEB5 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G), FASTA

>9H2P_1 Low conductance mechanosensitive channel YnaI (chains A, B, C, D, E, F, G)
AELFTNNALNLVIIFGSCAALILMSFWFRRGNRKRKGFLFHAVQFLIYTIIISAVGSIIN
YVIENYKLKFITPGVIDFICTSLIAVILTIKLFLLINQFEKQQAAKGRDITSARIMSRII
KITIIVVLVLLYGEHFGMSLSGLLTFGGIGGLAVGMAGKDILSNFFSGIMLYFDRPFSIG
DWIRSPDRNIEGTVAEIGWRITKITTFDNRPLYVPNSLFSSISVENPGRMTNRRITTTIG
LRYEDAAKVGVIVEAVREMLKNHPAIDQRQTLLVYFNQFADSSLNIMVYCFTKTTVWAEW
LAAQQDVYLKIIDIVQSHGADFAFPSQTLYMD

Ligands and cofactors

ID	Name	Formula	Copies
D12	Dodecane	C12 H26	42

Primary citation

Mechanosensitive channel engineering: A study on the mixing and matching of YnaI and MscS sensor paddles and pores. Flegler, V.J., Rasmussen, A., Hedrich, R. et al. Nat Commun (2025) 16:7881-7881. DOI 10.1038/s41467-025-63253-0 · PubMed

Other PDB entries of the same protein (UniProt P0AEB5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9H95 2.2 Å, YnaI in closed conformation purified in DDM with additional lipids showing ligand-filled…
9E63 2.3 Å, Cryo-EM structure of mechanosensitive channel YnaI in DOPC nanodiscs treated with…
9E67 2.3 Å, Cryo-EM structure of mechanosensitive channel YnaI in DDPC nanodiscs
7N4T 2.4 Å, Low conductance mechanosensitive channel YnaI
9E62 2.5 Å, Cryo-EM structure of mechanosensitive channel YnaI in DOPC nanodiscs
9E68 2.5 Å, Cryo-EM structure of MscS/YnaI chimera in DOPC nanodiscs
9H2S 2.7 Å, a YnaI-MscS chimera in a closed conformation purified in DDM with additional lipids…
9E65 2.8 Å, Cryo-EM structure of mechanosensitive channel YnaI A155V mutant in conformation 1
9E66 2.8 Å, Cryo-EM structure of mechanosensitive channel YnaI A155V mutant in conformation 2
9H2V 2.8 Å, a YnaI-MscS chimera in an open conformation purified in DDM showing ligand-filled pockets
6ZYD 3.0 Å, YnaI
9E64 3.0 Å, Cryo-EM structure of mechanosensitive channel YnaI in DOPC nanodiscs treated with…

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