9H2S: PDB entry 9H2S

a YnaI-MscS chimera in a closed conformation purified in DDM with additional lipids showing ligand-filled pore and pockets. Determined by electron microscopy at 2.7 Å resolution. Released 24 Sept 2025.

Method: Electron microscopy
Resolution: 2.7 Å
Organism: Escherichia coli (strain K12)
Chains: 7
Atoms: 18,235
Mol. weight: 258.72 kDa
Ligands: D12
Released: 24 Sept 2025

Explore 9H2S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9H2S contains 91 α-helices and 63 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: 13 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	6-31	26
α-helix	41-53	13
α-helix	54-58	5
α-helix	59-67	9
α-helix	75-108	34
α-helix	112-133	22
α-helix	143-159	17
α-helix	161-175	15
β-strand	184-186	3	1
β-strand	191-197	7	1
β-strand	201-205	5	1
β-strand	211-215	5	1
α-helix	216-220	5
β-strand	224-226	3	1
β-strand	232-241	10	2
α-helix	247-259	13
β-strand	271-277	7	2
β-strand	282-291	10	2
α-helix	292-294	3
α-helix	295-313	19
α-helix	317-320	4
β-strand	321-327	7	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Low conductance mechanosensitive channel YnaI,Small-conductance mechanosensitive channel	A, B, C, D, E, F, G	protein	327	Escherichia coli (strain K12)	P0AEB5 (AlphaFold model), P0C0S1 (AlphaFold model)

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

>9H2S_1 Low conductance mechanosensitive channel YnaI,Small-conductance mechanosensitive channel (chains A, B, C, D, E, F, G)
AELFTNNALNLVIIFGSCAALILMSFWFRRGNRKRKGFLFHAVQFLIYTIIISAVGSIIN
YVIENYKLKFITPGVIDFICTSLIAVILTIKLFLLINQFEKQQIKKGRDITSARIMSRII
KITIIVVLVLLYGEHFGVQTASVIAVLGAAGLAVGLALQGSLSNLAAGVLLVMFRPFRAG
EYVDLGGVAGTVLSVQIFSTTMRTADGKIIVIPNGKIIAGNIINFSREPVRRNEFIIGVA
YDSDIDQVKQILTNIIQSEDRILKDREMTVRLNELGASSINFVVRVWSNSGDLQNVYWDV
LERIKREFDAAGISFPYPQMDVNFKRV

Ligands and cofactors

ID	Name	Formula	Copies
D12	Dodecane	C12 H26	21

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
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
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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