6ZYE: YnaI in an open-like conformation

YnaI in an open-like conformation. Determined by electron microscopy at 4.1 Å resolution. Released 25 Nov 2020.

Method: Electron microscopy
Resolution: 4.1 Å
Organism: Escherichia coli (strain K12)
Chains: 7
Atoms: 11,592
Mol. weight: 300.49 kDa
Released: 25 Nov 2020

Explore 6ZYE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6ZYE contains 56 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: 8 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	-34--17	18
α-helix	150-159	10
α-helix	161-175	15
β-strand	184-186	3	1
β-strand	193-198	6	1
β-strand	203-208	6	1
β-strand	213-217	5	1
α-helix	218-223	6
β-strand	226-227	2	1
α-helix	229-231	3
β-strand	235-243	9	5
α-helix	245-250	6
α-helix	251-263	13
β-strand	268	1	5
β-strand	274-275	2	5
β-strand	278-282	5	5
β-strand	285-294	10	5
α-helix	299-320	22
β-strand	324	1	5
β-strand	328-332	5	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
YnaI,Low conductance mechanosensitive channel YnaI	A, B, C, D, E, F, G	protein	387	Escherichia coli (strain K12)	P0AEB5 (AlphaFold model)

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

>6ZYE_1 YnaI,Low conductance mechanosensitive channel YnaI (chains A, B, C, D, E, F, G)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXMIAELFTNNALNLVIIFGSCAALI
LMSFWFRRGNRKRKGFLFHAVQFLIYTIIISAVGSIINYVIENYKLKFITPGVIDFICTS
LIAVILTIKLFLLINQFEKQQIKKGRDITSARIMSRIIKITIIVVLVLLYGEHFGMSLSG
LLTFGGIGGLAVGMAGKDILSNFFSGIMLYFDRPFSIGDWIRSPDRNIEGTVAEIGWRIT
KITTFDNRPLYVPNSLFSSISVENPGRMTNRRITTTIGLRYEDAAKVGVIVEAVREMLKN
HPAIDQRQTLLVYFNQFADSSLNIMVYCFTKTTVWAEWLAAQQDVYLKIIDIVQSHGADF
AFPSQTLYMDNITPPEQGRLEHHHHHH

Primary citation

The MscS-like channel YnaI has a gating mechanism based on flexible pore helices. Flegler, V.J., Rasmussen, A., Rao, S. et al. Proc Natl Acad Sci U S A (2020) 117:28754-28762. DOI 10.1073/pnas.2005641117 · 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
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

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