8DDJ: Open MscS in PC14.1 Nanodiscs

Open MscS in PC14.1 Nanodiscs. Determined by electron microscopy at 3.1 Å resolution. Released 15 Feb 2023.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Escherichia coli K-12
Chains: 7
Atoms: 14,903
Mol. weight: 211.95 kDa
Released: 15 Feb 2023

Explore 8DDJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8DDJ contains 77 α-helices and 69 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, F and G: 11 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	11-13	3
α-helix	16-19	4
α-helix	21-58	38
α-helix	63-89	27
α-helix	94-111	18
α-helix	113-127	15
β-strand	135-137	3	1
β-strand	142-148	7	1
β-strand	152-156	5	1
β-strand	162-166	5	1
α-helix	167-172	6
β-strand	175-177	3	1
β-strand	183-192	10	2
α-helix	198-210	13
β-strand	215	1	2
β-strand	222-228	7	2
β-strand	233-242	10	2
α-helix	243-245	3
α-helix	246-264	19
α-helix	268-270	3
β-strand	272-279	8	3

Chain B: 11 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	11-13	3
α-helix	16-19	4
α-helix	21-58	38
α-helix	63-89	27
α-helix	94-111	18
α-helix	113-127	15
β-strand	135-137	3	1
β-strand	142-148	7	1
β-strand	152-156	5	1
β-strand	162-166	5	1
α-helix	167-172	6
β-strand	175-177	3	1
β-strand	183-192	10	4
α-helix	198-210	13
β-strand	215	1	4
β-strand	222-228	7	4
β-strand	233-242	10	4
α-helix	243-245	3
α-helix	246-264	19
α-helix	266-270	5
β-strand	272-279	8	3

Chain C: 11 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	11-13	3
α-helix	16-19	4
α-helix	21-58	38
α-helix	63-89	27
α-helix	95-111	17
α-helix	113-127	15
β-strand	135-137	3	1
β-strand	142-148	7	1
β-strand	152-156	5	1
β-strand	162-166	5	1
α-helix	167-172	6
β-strand	175-177	3	1
β-strand	183-192	10	5
α-helix	198-210	13
β-strand	215	1	5
β-strand	222-228	7	5
β-strand	233-242	10	5
α-helix	243-245	3
α-helix	246-264	19
α-helix	266-271	6
β-strand	272-279	8	3

Chain D: 11 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	11-13	3
α-helix	16-19	4
α-helix	21-58	38
α-helix	63-89	27
α-helix	95-111	17
α-helix	113-127	15
β-strand	135-137	3	1
β-strand	142-148	7	1
β-strand	152-156	5	1
β-strand	162-166	5	1
α-helix	167-172	6
β-strand	175-177	3	1
β-strand	183-192	10	6
α-helix	198-210	13
β-strand	215	1	6
β-strand	222-228	7	6
β-strand	233-242	10	6
α-helix	243-245	3
α-helix	246-264	19
α-helix	268-270	3
β-strand	272-279	8	3

Chain E: 11 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	11-13	3
α-helix	16-19	4
α-helix	21-58	38
α-helix	63-89	27
α-helix	94-111	18
α-helix	113-127	15
β-strand	135-137	3	1
β-strand	142-148	7	1
β-strand	152-156	5	1
β-strand	162-166	5	1
α-helix	167-172	6
β-strand	175-177	3	1
β-strand	183-192	10	7
α-helix	198-210	13
β-strand	222-228	7	7
β-strand	233-242	10	7
α-helix	243-245	3
α-helix	246-264	19
α-helix	266-271	6
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	280	Escherichia coli K-12	P0C0S1 (AlphaFold model)

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

>8DDJ_1 Mechanosensitive channel MscS (chains A, B, C, D, E, F, G)
MEDLNVVDSINGAGSWLVANQALLLSYAVNIVAALAIIIVGLIIARMISNAVNRLMISRK
IDATVADFLSALVRYGIIAFTLIAALGRVGVQTASVIAVLGAAGLAVGLALQGSLSNLAA
GVLLVMFRPFRAGEYVDLGGVAGTVLSVQIFSTTMRTADGKIIVIPNGKIIAGNIINFSR
EPVRRNEFIIGVAYDSDIDQVKQILTNIIQSEDRILKDREMTVRLNELGASSINFVVRVW
SNSGDLQNVYWDVLERIKREFDAAGISFPYPQMDVNFKRV

Primary citation

State-specific morphological deformations of the lipid bilayer explain mechanosensitive gating of MscS ion channels. Park, Y.C., Reddy, B., Bavi, N. et al. Elife (2023) 12. DOI 10.7554/eLife.81445 · 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
6VYK 3.2 Å, Cryo-EM structure of mechanosensitive channel MscS in PC-18:1 nanodiscs
6UZH 3.3 Å, Cryo-EM structure of mechanosensitive channel MscS reconstituted into peptidiscs

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