9E67: Mechanosensitive channel YnaI in DDPC nanodiscs

Cryo-EM structure of mechanosensitive channel YnaI in DDPC nanodiscs. Determined by electron microscopy at 2.3 Å resolution. Released 27 Aug 2025.

Method: Electron microscopy
Resolution: 2.3 Å
Organism: Escherichia coli
Chains: 7
Atoms: 19,033
Mol. weight: 304.03 kDa
Ligands: PTY
Released: 27 Aug 2025

Explore 9E67 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9E67 contains 91 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 and B: 13 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	6-11	6
α-helix	16-31	16
α-helix	41-67	27
α-helix	75-108	34
α-helix	112-134	23
α-helix	142-159	18
α-helix	161-175	15
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	218-222	5
β-strand	226-227	2	2
α-helix	229-231	3
β-strand	235-243	9	3
α-helix	245-247	3
α-helix	251-262	12
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	325-327	3
β-strand	328-333	6	4

Chain C: 13 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	6-11	6
α-helix	16-31	16
α-helix	41-67	27
α-helix	75-108	34
α-helix	112-133	22
α-helix	142-159	18
α-helix	161-175	15
β-strand	184-185	2	7
β-strand	186	1	5
β-strand	194-199	6	7
β-strand	203-207	5	7
β-strand	213-217	5	7
α-helix	218-222	5
β-strand	226-227	2	5
α-helix	229-231	3
β-strand	235-243	9	8
α-helix	245-247	3
α-helix	251-264	14
β-strand	268	1	8
β-strand	275-281	7	8
β-strand	286-294	9	8
α-helix	299-319	21
β-strand	324	1	8
α-helix	325-327	3
β-strand	328-333	6	4

Chains D, E, F and G: 13 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	6-11	6
α-helix	16-31	16
α-helix	41-67	27
α-helix	75-108	34
α-helix	112-134	23
α-helix	142-159	18
α-helix	161-175	15
β-strand	184-185	2	9
β-strand	186	1	7
β-strand	194-199	6	9
β-strand	203-207	5	9
β-strand	213-217	5	9
α-helix	218-222	5
β-strand	226-227	2	7
α-helix	229-231	3
β-strand	235-243	9	10
α-helix	245-247	3
α-helix	251-264	14
β-strand	268	1	10
β-strand	275-281	7	10
β-strand	286-294	9	10
α-helix	299-319	21
β-strand	324	1	10
α-helix	325-327	3
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	351	Escherichia coli	P0AEB5 (AlphaFold model)

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

>9E67_1 Low conductance mechanosensitive channel YnaI (chains A, B, C, D, E, F, G)
MIAELFTNNALNLVIIFGSCAALILMSFWFRRGNRKRKGFLFHAVQFLIYTIIISAVGSI
INYVIENYKLKFITPGVIDFICTSLIAVILTIKLFLLINQFEKQQIKKGRDITSARIMSR
IIKITIIVVLVLLYGEHFGMSLSGLLTFGGIGGLAVGMAGKDILSNFFSGIMLYFDRPFS
IGDWIRSPDRNIEGTVAEIGWRITKITTFDNRPLYVPNSLFSSISVENPGRMTNRRITTT
IGLRYEDAAKVGVIVEAVREMLKNHPAIDQRQTLLVYFNQFADSSLNIMVYCFTKTTVWA
EWLAAQQDVYLKIIDIVQSHGADFAFPSQTLYMDNITPPEQGRAAHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
PTY	Phosphatidylethanolamine	C40 H80 N O8 P	35

Primary citation

Lipid interactions and gating hysteresis suggest a physiological role for mechanosensitive channel YnaI. Will, N., Hiotis, G., Nakayama, Y. et al. Nat Commun (2025) 16:7472-7472. DOI 10.1038/s41467-025-62805-8 · 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…
9H2P 2.3 Å, YnaI in its open conformation purified in DDM showing ligand-filled pockets
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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