7N4T: Low conductance mechanosensitive channel YnaI

Low conductance mechanosensitive channel YnaI. Determined by electron microscopy at 2.4 Å resolution. Released 20 Apr 2022.

Method: Electron microscopy
Resolution: 2.4 Å
Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
Chains: 7
Atoms: 12,887
Mol. weight: 276.75 kDa
Ligands: PEE
Released: 20 Apr 2022

Explore 7N4T in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7N4T contains 60 α-helices and 102 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.

Chain A: 8 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	112-138	27
α-helix	142-175	34
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
α-helix	225	1
β-strand	226-227	2	2
α-helix	229-231	3
β-strand	236-240	5	3
β-strand	243	1	4
α-helix	251-264	14
β-strand	268	1	5
β-strand	275-278	4	3
β-strand	286	1	4
β-strand	288-293	6	3
β-strand	294	1	5
α-helix	301-319	19
β-strand	324	1	4
α-helix	325-326	2

Chain B: 8 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	112-138	27
α-helix	142-175	34
β-strand	184-185	2	2
β-strand	186	1	6
β-strand	194-199	6	2
β-strand	203-207	5	2
β-strand	213-217	5	2
α-helix	218-222	5
α-helix	225	1
β-strand	226-227	2	6
α-helix	229-231	3
β-strand	235-240	6	7
β-strand	243	1	8
α-helix	248-250	3
α-helix	251-263	13
β-strand	268	1	7
β-strand	275-278	4	7
β-strand	286	1	8
β-strand	288-294	7	7
α-helix	301-319	19
β-strand	330	1	9
β-strand	335	1	10

Chain C: 10 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	113-138	26
α-helix	142-175	34
β-strand	184-185	2	6
β-strand	186	1	11
β-strand	194-199	6	6
β-strand	203-207	5	6
β-strand	213-217	5	6
α-helix	218-222	5
α-helix	225	1
β-strand	226-227	2	11
α-helix	229-231	3
β-strand	235-240	6	12
β-strand	243	1	13
α-helix	248-250	3
α-helix	251-264	14
β-strand	268	1	12
β-strand	275-278	4	12
β-strand	286	1	13
β-strand	288-294	7	12
α-helix	301-319	19
α-helix	323	1
β-strand	324	1	13
α-helix	325	1
β-strand	328	1	9
β-strand	333	1	10
β-strand	335	1	14

Chain D: 8 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	113-133	21
α-helix	142-175	34
β-strand	184-185	2	11
β-strand	186	1	15
β-strand	194-199	6	11
β-strand	203-207	5	11
β-strand	213-217	5	11
α-helix	218-222	5
α-helix	225	1
β-strand	226-227	2	15
α-helix	229-231	3
β-strand	235-240	6	16
β-strand	243	1	17
α-helix	248-250	3
α-helix	251-264	14
β-strand	268	1	16
β-strand	275-278	4	16
β-strand	286	1	17
β-strand	288-294	7	16
α-helix	301-319	19
β-strand	333	1	14
β-strand	335	1	18

Chain E: 9 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	112-133	22
α-helix	135-138	4
α-helix	142-175	34
β-strand	184-185	2	15
β-strand	186	1	19
β-strand	194-199	6	15
β-strand	203-207	5	15
β-strand	213-217	5	15
α-helix	218-222	5
α-helix	225	1
β-strand	226-227	2	19
α-helix	229-231	3
β-strand	235-240	6	20
β-strand	243	1	21
α-helix	248-250	3
α-helix	251-264	14
β-strand	268	1	20
β-strand	275-278	4	20
β-strand	286	1	21
β-strand	288-294	7	20
α-helix	301-319	19
β-strand	324	1	21
β-strand	333	1	18
β-strand	335	1	22

Chain F: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	112-138	27
α-helix	142-159	18
α-helix	162-175	14
β-strand	184-185	2	19
β-strand	186	1	23
β-strand	194-199	6	19
β-strand	203-207	5	19
β-strand	213-217	5	19
α-helix	218-222	5
α-helix	225	1
β-strand	226-227	2	23
α-helix	229-231	3
β-strand	236-240	5	24
β-strand	243	1	25
α-helix	248-263	16
β-strand	268	1	26
β-strand	275-278	4	24
β-strand	286	1	25
β-strand	288-293	6	24
β-strand	294	1	26
α-helix	301-319	19
β-strand	333	1	22
β-strand	335	1	27

Chain G: 9 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	112-138	27
α-helix	142-175	34
β-strand	184-185	2	23
β-strand	186	1	1
β-strand	194-199	6	23
β-strand	203-207	5	23
β-strand	213-217	5	23
α-helix	218-222	5
α-helix	225	1
β-strand	226-227	2	1
α-helix	229-231	3
β-strand	235-240	6	28
β-strand	243	1	29
α-helix	248-250	3
α-helix	251-264	14
β-strand	268	1	28
β-strand	275-278	4	28
β-strand	286	1	29
β-strand	288-294	7	28
α-helix	301-319	19
β-strand	324	1	29
α-helix	325-326	2
β-strand	333	1	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Low conductance mechanosensitive channel YnaI	A, B, C, D, E, F, G	protein	343	Escherichia coli 'BL21-Gold(DE3)pLysS AG'	P0AEB5 (AlphaFold model)

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

>7N4T_1 Low conductance mechanosensitive channel YnaI (chains A, B, C, D, E, F, G)
MIAELFTNNALNLVIIFGSCAALILMSFWFRRGNRKRKGFLFHAVQFLIYTIIISAVGSI
INYVIENYKLKFITPGVIDFICTSLIAVILTIKLFLLINQFEKQQIKKGRDITSARIMSR
IIKITIIVVLVLLYGEHFGMSLSGLLTFGGIGGLAVGMAGKDILSNFFSGIMLYFDRPFS
IGDWIRSPDRNIEGTVAEIGWRITKITTFDNRPLYVPNSLFSSISVENPGRMTNRRITTT
IGLRYEDAAKVGVIVEAVREMLKNHPAIDQRQTLLVYFNQFADSSLNIMVYCFTKTTVWA
EWLAAQQDVYLKIIDIVQSHGADFAFPSQTLYMDNITPPEQGR

Ligands and cofactors

ID	Name	Formula	Copies
PEE	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine	C41 H78 N O8 P	7

Primary citation

Cryo-EM Structure of Mechanosensitive Channel YnaI Using SMA2000: Challenges and Opportunities. Catalano, C., Ben-Hail, D., Qiu, W. et al. Membranes (Basel) (2021) 11. DOI 10.3390/membranes11110849 · 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
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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