8F6Y: Torpedo nicotinic acetylcholine receptor
Cryo-EM structure of Torpedo nicotinic acetylcholine receptor in complex with etomidate, desensitized-like state. Determined by electron microscopy at 2.79 Å resolution. Released 7 Jun 2023.
- Method
- Electron microscopy
- Resolution
- 2.79 Å
- Organism
- Tetronarce californica
- Chains
- 5
- Atoms
- 17,053
- Mol. weight
- 277.89 kDa
- Ligands
- CHT, V8D, DD9, POV
- Released
- 7 Jun 2023
Explore 8F6Y in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8F6Y contains 77 α-helices and 89 β-strands across 5 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: 16 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-11 | 10 | |
| β-strand | 29-44 | 16 | 1 |
| β-strand | 49-61 | 13 | 1 |
| α-helix | 63-65 | 3 | |
| α-helix | 69-72 | 4 | |
| β-strand | 77-81 | 5 | 1 |
| α-helix | 82-84 | 3 | |
| β-strand | 90-92 | 3 | 2 |
| β-strand | 95 | 1 | 1 |
| β-strand | 107-111 | 5 | 1 |
| β-strand | 115-118 | 4 | 1 |
| β-strand | 121-127 | 7 | 1 |
| α-helix | 129-131 | 3 | |
| β-strand | 139-148 | 10 | 2 |
| β-strand | 156-160 | 5 | 1 |
| β-strand | 166 | 1 | 1 |
| α-helix | 170-172 | 3 | |
| β-strand | 176-188 | 13 | 2 |
| β-strand | 198-209 | 12 | 2 |
| α-helix | 213-214 | 2 | |
| α-helix | 215-219 | 5 | |
| α-helix | 220-226 | 7 | |
| α-helix | 231-234 | 4 | |
| α-helix | 237-239 | 3 | |
| α-helix | 242-261 | 20 | |
| α-helix | 273-299 | 27 | |
| α-helix | 310-318 | 9 | |
| α-helix | 320-323 | 4 | |
| β-strand | 329 | 1 | 3 |
| α-helix | 371-425 | 55 | |
Chain B: 14 helices, 19 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-9 | 7 | |
| α-helix | 10-14 | 5 | |
| β-strand | 31-46 | 16 | 4 |
| β-strand | 51-63 | 13 | 4 |
| α-helix | 65-67 | 3 | |
| β-strand | 80-82 | 3 | 4 |
| β-strand | 92-94 | 3 | 5 |
| β-strand | 97 | 1 | 4 |
| β-strand | 110-112 | 3 | 4 |
| β-strand | 117-120 | 4 | 4 |
| β-strand | 123-129 | 7 | 4 |
| β-strand | 141-150 | 10 | 5 |
| β-strand | 158-162 | 5 | 4 |
| α-helix | 163 | 1 | |
| β-strand | 164-166 | 3 | 6 |
| β-strand | 171-173 | 3 | 6 |
| β-strand | 176 | 1 | 7 |
| β-strand | 178 | 1 | 4 |
| β-strand | 185 | 1 | 4 |
| β-strand | 190-194 | 5 | 5 |
| β-strand | 196 | 1 | 7 |
| β-strand | 197-201 | 5 | 5 |
| β-strand | 213-223 | 11 | 5 |
| α-helix | 226-228 | 3 | |
| α-helix | 229-233 | 5 | |
| α-helix | 234-245 | 12 | |
| α-helix | 246-248 | 3 | |
| α-helix | 256-276 | 21 | |
| α-helix | 287-313 | 27 | |
| α-helix | 324-328 | 5 | |
| α-helix | 329-333 | 5 | |
| α-helix | 334-337 | 4 | |
| α-helix | 417-475 | 59 | |
Chain C: 17 helices, 21 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-11 | 10 | |
| β-strand | 29-44 | 16 | 8 |
| β-strand | 49-61 | 13 | 8 |
| α-helix | 69-72 | 4 | |
| β-strand | 77-80 | 4 | 8 |
| α-helix | 82-84 | 3 | |
| β-strand | 90-92 | 3 | 9 |
| β-strand | 95 | 1 | 8 |
| β-strand | 104 | 1 | 8 |
| α-helix | 106-107 | 2 | |
| β-strand | 108-111 | 4 | 8 |
| β-strand | 115-118 | 4 | 8 |
| β-strand | 121-127 | 7 | 8 |
| β-strand | 139-148 | 10 | 9 |
| β-strand | 156-160 | 5 | 8 |
| α-helix | 161 | 1 | |
| β-strand | 162 | 1 | 10 |
| β-strand | 169 | 1 | 10 |
| β-strand | 172 | 1 | 11 |
| β-strand | 174 | 1 | 8 |
| α-helix | 177-179 | 3 | |
| β-strand | 181 | 1 | 8 |
| β-strand | 186-190 | 5 | 9 |
| β-strand | 192 | 1 | 11 |
| β-strand | 193-196 | 4 | 9 |
| β-strand | 206-215 | 10 | 9 |
| α-helix | 218-220 | 3 | |
| α-helix | 221-225 | 5 | |
| α-helix | 226-237 | 12 | |
| α-helix | 243-245 | 3 | |
| α-helix | 248-266 | 19 | |
| α-helix | 279-305 | 27 | |
| β-strand | 312 | 1 | 12 |
| α-helix | 316-319 | 4 | |
| α-helix | 320-325 | 6 | |
| α-helix | 326-330 | 5 | |
| α-helix | 333-336 | 4 | |
| α-helix | 399-459 | 61 | |
Chain D: 17 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-11 | 10 | |
| β-strand | 29-44 | 16 | 13 |
| β-strand | 49-61 | 13 | 13 |
| α-helix | 63-65 | 3 | |
| α-helix | 69-72 | 4 | |
| β-strand | 77-81 | 5 | 13 |
| α-helix | 82-84 | 3 | |
| β-strand | 90-92 | 3 | 14 |
| β-strand | 95 | 1 | 13 |
| β-strand | 107-111 | 5 | 13 |
| β-strand | 115-118 | 4 | 13 |
| β-strand | 121-127 | 7 | 13 |
| β-strand | 139-148 | 10 | 14 |
| β-strand | 156-160 | 5 | 13 |
| β-strand | 166 | 1 | 13 |
| α-helix | 170 | 1 | |
| β-strand | 171 | 1 | 13 |
| α-helix | 172 | 1 | |
| β-strand | 176-188 | 13 | 14 |
| β-strand | 198-209 | 12 | 14 |
| α-helix | 212-214 | 3 | |
| α-helix | 215-219 | 5 | |
| α-helix | 220-228 | 9 | |
| α-helix | 229-234 | 6 | |
| α-helix | 237-239 | 3 | |
| α-helix | 242-261 | 20 | |
| α-helix | 273-299 | 27 | |
| α-helix | 310-313 | 4 | |
| α-helix | 314-319 | 6 | |
| α-helix | 320-323 | 4 | |
| β-strand | 329 | 1 | 12 |
| α-helix | 371-425 | 55 | |
Chain E: 13 helices, 20 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-12 | 9 | |
| β-strand | 29-44 | 16 | 15 |
| β-strand | 49-61 | 13 | 15 |
| α-helix | 69-72 | 4 | |
| β-strand | 77-81 | 5 | 15 |
| α-helix | 82-84 | 3 | |
| β-strand | 90-92 | 3 | 16 |
| β-strand | 95 | 1 | 15 |
| β-strand | 107-111 | 5 | 15 |
| β-strand | 115-118 | 4 | 15 |
| β-strand | 121-127 | 7 | 15 |
| α-helix | 129-131 | 3 | |
| β-strand | 139-148 | 10 | 16 |
| β-strand | 156-160 | 5 | 15 |
| β-strand | 162-163 | 2 | 17 |
| β-strand | 166-167 | 2 | 17 |
| β-strand | 170 | 1 | 18 |
| β-strand | 172-173 | 2 | 15 |
| β-strand | 179 | 1 | 15 |
| β-strand | 184-188 | 5 | 16 |
| β-strand | 190 | 1 | 18 |
| β-strand | 191-195 | 5 | 16 |
| β-strand | 207-217 | 11 | 16 |
| α-helix | 220-222 | 3 | |
| α-helix | 223-227 | 5 | |
| α-helix | 228-234 | 7 | |
| α-helix | 237-241 | 5 | |
| α-helix | 251-271 | 21 | |
| α-helix | 282-308 | 27 | |
| β-strand | 315 | 1 | 3 |
| α-helix | 319-326 | 8 | |
| α-helix | 328-332 | 5 | |
| α-helix | 412-471 | 60 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Acetylcholine receptor subunit alpha | A, D | protein | 433 | Tetronarce californica | P02710 (AlphaFold model) |
| Acetylcholine receptor subunit delta | B | protein | 500 | Tetronarce californica | P02718 (AlphaFold model) |
| Acetylcholine receptor subunit beta | C | protein | 469 | Tetronarce californica | P02712 (AlphaFold model) |
| Acetylcholine receptor subunit gamma | E | protein | 489 | Tetronarce californica | P02714 (AlphaFold model) |
Sequence of entity 1 (A, D), FASTA
>8F6Y_1 Acetylcholine receptor subunit alpha (chains A, D)
SEHETRLVANLLENYNKVIRPVEHHTHFVDITVGLQLIQLISVDEVNQIVETNVRLRQQW
IDVRLRWNPADYGGIKKIRLPSDDVWLPDLVLYNNADGDFAIVHMTKLLLDYTGKIMWTP
PAIFKSYCEIIVTHFPFDQQNCTMKLGIWTYDGTKVSISPESDRPDLSTFMESGEWVMKD
YRGWKHWVYYTCCPDTPYLDITYHFIMQRIPLYFVVNVIIPCLLFSFLTGLVFYLPTDSG
EKMTLSISVLLSLTVFLLVIVELIPSTSSAVPLIGKYMLFTMIFVISSIIITVVVINTHH
RSPSTHTMPQWVRKIFIDTIPNVMFFSTMKRASKEKQENKIFADDIDISDISGKQVTGEV
IFQTPLIKNPDVKSAIEGVKYIAEHMKSDEESSNAAEEWKYVAMVIDHILLCVFMLICII
GTVSVFAGRLIEL
Sequence of entity 2 (B), FASTA
>8F6Y_2 Acetylcholine receptor subunit delta (chains B)
VNEEERLINDLLIVNKYNKHVRPVKHNNEVVNIALSLTLSNLISLKETDETLTSNVWMDH
AWYDHRLTWNASEYSDISILRLPPELVWIPDIVLQNNNDGQYHVAYFCNVLVRPNGYVTW
LPPAIFRSSCPINVLYFPFDWQNCSLKFTALNYDANEITMDLMTDTIDGKDYPIEWIIID
PEAFTENGEWEIIHKPAKKNIYPDKFPNGTNYQDVTFYLIIRRKPLFYVINFITPCVLIS
FLASLAFYLPAESGEKMSTAISVLLAQAVFLLLTSQRLPETALAVPLIGKYLMFIMSLVT
GVIVNCGIVLNFHFRTPSTHVLSTRVKQIFLEKLPRILHMSRADESEQPDWQNDLKLRRS
SSVGYISKAQEYFNIKSRSELMFEKQSERHGLVPRVTPRIGFGNNNENIAASDQLHDEIK
SGIDSTNYIVKQIKEKNAYDEEVGNWNLVGQTIDRLSMFIITPVMVLGTIFIFVMGNFNH
PPAKPFEGDPFDYSSDHPRC
Sequence of entity 3 (C), FASTA
>8F6Y_3 Acetylcholine receptor subunit beta (chains C)
SVMEDTLLSVLFETYNPKVRPAQTVGDKVTVRVGLTLTNLLILNEKIEEMTTNVFLNLAW
TDYRLQWDPAAYEGIKDLRIPSSDVWQPDIVLMNNNDGSFEITLHVNVLVQHTGAVSWQP
SAIYRSSCTIKVMYFPFDWQNCTMVFKSYTYDTSEVTLQHALDAKGEREVKEIVINKDAF
TENGQWSIEHKPSRKNWRSDDPSYEDVTFYLIIQRKPLFYIVYTIIPCILISILAILVFY
LPPDAGEKMSLSISALLAVTVFLLLLADKVPETSLSVPIIIRYLMFIMILVAFSVILSVV
VLNLHHRSPNTHTMPNWIRQIFIETLPPFLWIQRPVTTPSPDSKPTIISRANDEYFIRKP
AGDFVCPVDNARVAVQPERLFSEMKWHLNGLTQPVTLPQDLKEAVEAIKYIAEQLESASE
FDDLKKDWQYVAMVADRLFLYVFFVICSIGTFSIFLDASHNVPPDNPFA
Sequence of entity 4 (E), FASTA
>8F6Y_4 Acetylcholine receptor subunit gamma (chains E)
ENEEGRLIEKLLGDYDKRIIPAKTLDHIIDVTLKLTLTNLISLNEKEEALTTNVWIEIQW
NDYRLSWNTSEYEGIDLVRIPSELLWLPDVVLENNVDGQFEVAYYANVLVYNDGSMYWLP
PAIYRSTCPIAVTYFPFDWQNCSLVFRSQTYNAHEVNLQLSAEEGEAVEWIHIDPEDFTE
NGEWTIRHRPAKKNYNWQLTKDDTDFQEIIFFLIIQRKPLFYIINIIAPCVLISSLVVLV
YFLPAQAGGQKCTLSISVLLAQTIFLFLIAQKVPETSLNVPLIGKYLIFVMFVSMLIVMN
CVIVLNVSLRTPNTHSLSEKIKHLFLGFLPKYLGMQLEPSEETPEKPQPRRRSSFGIMIK
AEEYILKKPRSELMFEEQKDRHGLKRVNKMTSDIDIGTTVDLYKDLANFAPEIKSCVEAC
NFIAKSTKEQNDSGSENENWVLIGKVIDKACFWIALLLFSIGTLAIFLTGHFNQVPEFPF
PGDPRKYVP
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| CHT | Choline ion | C5 H14 N O | 2 |
| V8D | Etomidate | C14 H16 N2 O2 | 2 |
| DD9 | nonane | C9 H20 | 1 |
| POV | (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl… | C42 H82 N O8 P | 6 |
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 2 |
| CLR | Cholesterol | C27 H46 O | 3 |
Primary citation
Structural interplay of anesthetics and paralytics on muscle nicotinic receptors. Goswami, U., Rahman, M.M., Teng, J. et al. Nat Commun (2023) 14:3169-3169. DOI 10.1038/s41467-023-38827-5 · PubMed
Other PDB entries of the same protein (UniProt P02710 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8YQN 2.27 Å, Torpedo acetylcholine receptor in complex with Erabutoxin A
- 7QL5 2.5 Å, Torpedo muscle-type nicotinic acetylcholine receptor - nicotine-bound conformation
- 7SMM 2.5 Å, Cryo-EM structure of Torpedo acetylcholine receptor in apo form
- 7SMT 2.56 Å, Cryo-EM structure of Torpedo acetylcholine receptor in complex with d-tubocurarine and…
- 6UWZ 2.69 Å, Cryo-EM structure of Torpedo acetylcholine receptor in complex with alpha-bungarotoxin
- 8F6Z 2.7 Å, Cryo-EM structure of Torpedo nicotinic acetylcholine receptor in complex with…
- 7SMQ 2.74 Å, Cryo-EM structure of Torpedo acetylcholine receptor in apo form with added cholesterol
- 7SMR 2.77 Å, Cryo-EM structure of Torpedo acetylcholine receptor in complex with carbachol,…
- 9E3E 2.8 Å, Torpedo muscle-type nicotinic acetylcholine receptor - Diliganded State
- 7QKO 2.9 Å, Torpedo muscle-type nicotinic acetylcholine receptor - Resting conformation
- 8ESK 2.9 Å, Cryo-EM structure of Torpedo nicotinic acetylcholine receptor in complex with…
- 8F2S 2.9 Å, Cryo-EM structure of Torpedo nicotinic acetylcholine receptor in complex with…
Browse structure collections
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