6VYK: Mechanosensitive channel MscS

Cryo-EM structure of mechanosensitive channel MscS in PC-18:1 nanodiscs. Determined by electron microscopy at 3.2 Å resolution. Released 10 Feb 2021.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Escherichia coli
Chains: 7
Atoms: 14,623
Mol. weight: 221.97 kDa
Ligands: PCW
Released: 10 Feb 2021

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

Secondary structure: helices and β-sheets

6VYK contains 63 α-helices and 70 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, C, E and F: 9 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	24-57	34
α-helix	63-89	27
α-helix	94-110	17
α-helix	112-126	15
β-strand	135-137	3	1
β-strand	142-148	7	1
β-strand	152-157	6	1
β-strand	162-166	5	1
α-helix	167-171	5
β-strand	175-177	3	1
β-strand	183-192	10	2
α-helix	198-211	14
β-strand	215	1	2
β-strand	222-228	7	2
β-strand	233-242	10	2
α-helix	246-264	19
α-helix	268-270	3
β-strand	273-279	7	3

Chain B: 9 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	24-57	34
α-helix	63-89	27
α-helix	94-110	17
α-helix	112-126	15
β-strand	135-137	3	1
β-strand	142-148	7	1
β-strand	152-157	6	1
β-strand	162-166	5	1
α-helix	167-171	5
β-strand	176-177	2	1
β-strand	183-192	10	4
α-helix	198-211	14
β-strand	215	1	4
β-strand	222-228	7	4
β-strand	233-242	10	4
α-helix	246-264	19
α-helix	268-270	3
β-strand	273-279	7	3

Chain D: 9 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	24-57	34
α-helix	63-89	27
α-helix	94-110	17
α-helix	112-126	15
β-strand	135-137	3	1
β-strand	142-148	7	1
β-strand	152-157	6	1
β-strand	162-166	5	1
α-helix	167-171	5
β-strand	175-177	3	1
β-strand	183-192	10	6
α-helix	198-211	14
β-strand	215	1	6
β-strand	222-228	7	6
β-strand	233-242	10	6
α-helix	246-264	19
α-helix	268-270	3
β-strand	275-279	5	3

Chain G: 9 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	24-57	34
α-helix	63-89	27
α-helix	94-110	17
α-helix	112-126	15
β-strand	135-137	3	1
β-strand	142-148	7	1
β-strand	152-157	6	1
β-strand	162-166	5	1
α-helix	167-171	5
β-strand	175-177	3	1
β-strand	183-192	10	9
α-helix	198-211	14
β-strand	215	1	9
β-strand	222-228	7	9
β-strand	233-242	10	9
α-helix	246-264	19
α-helix	268-270	3
β-strand	272-279	8	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mechanosensitive channel MscS	A, B, C, D, E, F, G	protein	286	Escherichia coli	P0C0S1 (AlphaFold model)

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

>6VYK_1 Mechanosensitive channel MscS (chains A, B, C, D, E, F, G)
MEDLNVVDSINGAGSWLVANQALLLSYAVNIVAALAIIIVGLIIARMISNAVNRLMISRK
IDATVADFLSALVRYGIIAFTLIAALGRVGVQTASVIAVLGAAGLAVGLALQGSLSNLAA
GVLLVMFRPFRAGEYVDLGGVAGTVLSVQIFSTTMRTADGKIIVIPNGKIIAGNIINFSR
EPVRRNEFIIGVAYDSDIDQVKQILTNIIQSEDRILKDREMTVRLNELGASSINFVVRVW
SNSGDLQNVYWDVLERIKREFDAAGISFPYPQMDVNFKRVKEDKAA

Ligands and cofactors

ID	Name	Formula	Copies
PCW	1,2-dioleoyl-sn-glycero-3-phosphocholine	C44 H85 N O8 P	7

Primary citation

Visualization of the mechanosensitive ion channel MscS under membrane tension. Zhang, Y., Daday, C., Gu, R.X. et al. Nature (2021) 590:509-514. DOI 10.1038/s41586-021-03196-w · PubMed

Other PDB entries of the same protein (UniProt P0C0S1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7ONJ 2.3 Å, Mechanosensitive channel MscS solubilized with LMNG in open conformation
9E68 2.5 Å, Cryo-EM structure of MscS/YnaI chimera in DOPC nanodiscs
7OOA 2.7 Å, Mechanosensitive channel MscS solubilized with LMNG in open conformation with added lipid
9H2S 2.7 Å, a YnaI-MscS chimera in a closed conformation purified in DDM with additional lipids…
9H2V 2.8 Å, a YnaI-MscS chimera in an open conformation purified in DDM showing ligand-filled pockets
6RLD 2.9 Å, Structure of the mechanosensitive channel mscs embedded in the membrane bilayer
5AJI 2.99 Å, MscS D67R1 high resolution
6PWN 3.1 Å, MscS Nanodisc with N-terminal His-Tag
7OO0 3.1 Å, Mechanosensitive channel MscS solubilized with DDM in open conformation
7OO6 3.1 Å, Mechanosensitive channel MscS solubilized with DDM in closed conformation with added lipid
8DDJ 3.1 Å, Open MscS in PC14.1 Nanodiscs
6UZH 3.3 Å, Cryo-EM structure of mechanosensitive channel MscS reconstituted into peptidiscs

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