5Y4O: MscS channel, YnaI

Cryo-EM structure of MscS channel, YnaI. Determined by electron microscopy at 3.8 Å resolution. Released 20 Mar 2019.

Method: Electron microscopy
Resolution: 3.8 Å
Organism: Escherichia coli O157:H7
Chains: 7
Atoms: 12,341
Mol. weight: 277.35 kDa
Released: 20 Mar 2019

Explore 5Y4O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5Y4O contains 56 α-helices and 96 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 and D: 8 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	115-137	23
α-helix	142-144	3
α-helix	145-175	31
β-strand	184	1	1
β-strand	195	1	1
β-strand	196-199	4	2
β-strand	204-206	3	2
β-strand	207	1	3
β-strand	213	1	3
α-helix	218-222	5
α-helix	229-231	3
β-strand	235-238	4	4
β-strand	243	1	5
α-helix	245-250	6
α-helix	251-264	14
β-strand	268	1	4
β-strand	274-277	4	4
β-strand	289-294	6	4
α-helix	299-319	21
β-strand	324	1	5
β-strand	328	1	6
β-strand	330	1	7

Chain E: 8 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	115-137	23
α-helix	142-144	3
α-helix	145-175	31
β-strand	184	1	26
β-strand	195	1	26
β-strand	196-199	4	27
β-strand	204-206	3	27
β-strand	207	1	28
β-strand	213	1	28
α-helix	218-222	5
α-helix	229-231	3
β-strand	235-238	4	29
β-strand	243	1	30
α-helix	245-250	6
α-helix	251-264	14
β-strand	268	1	29
β-strand	274-277	4	29
β-strand	289-294	6	29
α-helix	299-319	21
β-strand	324	1	30
β-strand	328	1	25
β-strand	330-331	2	31

Chain F: 8 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	115-137	23
α-helix	142-144	3
α-helix	145-175	31
β-strand	184	1	32
β-strand	195	1	32
β-strand	196-199	4	33
β-strand	204-206	3	33
β-strand	207	1	34
β-strand	213	1	34
α-helix	218-222	5
α-helix	229-231	3
β-strand	235-238	4	35
β-strand	243	1	36
α-helix	245-250	6
α-helix	251-264	14
β-strand	268	1	35
β-strand	274-277	4	35
β-strand	289-294	6	35
α-helix	299-319	21
β-strand	324	1	36
β-strand	328-329	2	31

Chain G: 8 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	115-137	23
α-helix	142-144	3
α-helix	145-175	31
β-strand	184	1	37
β-strand	195	1	37
β-strand	196-199	4	38
β-strand	204-206	3	38
β-strand	207	1	39
β-strand	213	1	39
α-helix	218-222	5
α-helix	229-231	3
β-strand	235-238	4	40
β-strand	243	1	41
α-helix	245-250	6
α-helix	251-264	14
β-strand	268	1	40
β-strand	274-277	4	40
β-strand	289-294	6	40
α-helix	299-319	21
β-strand	324	1	41
β-strand	330	1	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Low conductance mechanosensitive channel YnaI	A, B, C, D, E, F, G	protein	349	Escherichia coli O157:H7	P0AEB5 (AlphaFold model)

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

>5Y4O_1 Low conductance mechanosensitive channel YnaI (chains A, B, C, D, E, F, G)
MIAELFTNNALNLVIIFGSCAALILMSFWFRRGNRKRKGFLFHAVQFLIYTIIISAVGSI
INYVIENYKLKFITPGVIDFICTSLIAVILTIKLFLLINQFEKQQIKKGRDITSARIMSR
IIKITIIVVLVLLYGEHFGMSLSGLLTFGGIGGLAVGMAGKDILSNFFSGIMLYFDRPFS
IGDWIRSPDRNIEGTVAEIGWRITKITTFDNRPLYVPNSLFSSISVENPGRMTNRRITTT
IGLRYEDAAKVGVIVEAVREMLKNHPAIDQRQTLLVYFNQFADSSLNIMVYCFTKTTVWA
EWLAAQQDVYLKIIDIVQSHGADFAFPSQTLYMDNITPPEQGRHHHHHH

Primary citation

A binding-block ion selective mechanism revealed by a Na/K selective channel. Yu, J., Zhang, B., Zhang, Y. et al. Protein Cell (2018) 9:629-639. DOI 10.1007/s13238-017-0465-8 · 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…
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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