6URT: Low conductance mechanosensitive channel YnaI

Extended Sensor Paddles with Bound Lipids Revealed in Mechanosensitive Channel YnaI. Determined by electron microscopy at 3.27 Å resolution. Released 28 Oct 2020.

Method: Electron microscopy
Resolution: 3.27 Å
Organism: Escherichia coli (strain K12)
Chains: 7
Atoms: 18,263
Mol. weight: 276.8 kDa
Ligands: QGD
Released: 28 Oct 2020

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

Secondary structure: helices and β-sheets

6URT contains 77 α-helices and 91 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: 11 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	5-11	7
α-helix	13-30	18
α-helix	41-67	27
α-helix	76-107	32
α-helix	112-133	22
α-helix	142-159	18
α-helix	161-175	15
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
β-strand	226-227	2	6
α-helix	229-231	3
β-strand	236-240	5	7
β-strand	243	1	8
α-helix	251-263	13
β-strand	268	1	9
β-strand	275-278	4	7
β-strand	286	1	8
β-strand	288-293	6	7
β-strand	294	1	9
α-helix	301-317	17

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 (strain K12)	P0AEB5 (AlphaFold model)

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

>6URT_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
QGD	O-{(R)-hydroxy[(2R)-3-(icosyloxy)-2-(tetradecanoyloxy)propoxy]phosphoryl}-L-ser…	C40 H80 N O9 P	7

Primary citation

Extended Sensor Paddles with Bound Lipids Revealed in Mechanosensitive Channel YnaI. Hu, W., Wang, Z., Zheng, H. To be published.

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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