6ZYD: YnaI

YnaI. Determined by electron microscopy at 3.0 Å resolution. Released 25 Nov 2020.

Method: Electron microscopy
Resolution: 3.0 Å
Organism: Escherichia coli (strain K12)
Chains: 7
Atoms: 16,933
Mol. weight: 324.76 kDa
Ligands: PEE
Released: 25 Nov 2020

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

Secondary structure: helices and β-sheets

6ZYD contains 70 α-helices and 98 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: 10 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	-65--48	18
α-helix	-38--7	32
α-helix	80-107	28
α-helix	112-138	27
α-helix	142-175	34
β-strand	184-185	2	11
β-strand	186	1	6
β-strand	187	1	11
β-strand	190-199	10	11
β-strand	203-208	6	11
β-strand	213-217	5	11
α-helix	218-222	5
β-strand	226-227	2	6
α-helix	229-231	3
β-strand	235-243	9	12
α-helix	245-250	6
α-helix	251-262	12
β-strand	268	1	12
β-strand	274-282	9	12
β-strand	285-294	10	12
α-helix	299-320	22
β-strand	324	1	12
β-strand	328-329	2	13
β-strand	330-331	2	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Low conductance mechanosensitive channel YnaI,Low conductance mechanosensitive channel YnaI	A, B, C, D, E, F, G	protein	419	Escherichia coli (strain K12)	P0AEB5 (AlphaFold model)

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

>6ZYD_1 Low conductance mechanosensitive channel YnaI,Low conductance mechanosensitive channel YnaI (chains A, B, C, D, E, F, G)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXMIAELFTNNALNLVIIFGSCAALILMSFWFRRGNRKRKGFLFHAVQFLIYTI
IISAVGSIINYVIENYKLKFITPGVIDFICTSLIAVILTIKLFLLINQFEKQQIKKGRDI
TSARIMSRIIKITIIVVLVLLYGEHFGMSLSGLLTFGGIGGLAVGMAGKDILSNFFSGIM
LYFDRPFSIGDWIRSPDRNIEGTVAEIGWRITKITTFDNRPLYVPNSLFSSISVENPGRM
TNRRITTTIGLRYEDAAKVGVIVEAVREMLKNHPAIDQRQTLLVYFNQFADSSLNIMVYC
FTKTTVWAEWLAAQQDVYLKIIDIVQSHGADFAFPSQTLYMDNITPPEQGRLEHHHHHH

Ligands and cofactors

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

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
9E64 3.0 Å, Cryo-EM structure of mechanosensitive channel YnaI in DOPC nanodiscs treated with…

Browse structure collections

About this viewer

MolViewer shows 6ZYD directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.