8F6Z: Torpedo nicotinic acetylcholine receptor

Cryo-EM structure of Torpedo nicotinic acetylcholine receptor in complex with succinylcholine, desensitized-like state. Determined by electron microscopy at 2.7 Å resolution. Released 7 Jun 2023.

Method: Electron microscopy
Resolution: 2.7 Å
Organism: Tetronarce californica
Chains: 5
Atoms: 16,997
Mol. weight: 277.76 kDa
Ligands: SCK, CLR, NAG, POV
Released: 7 Jun 2023

Explore 8F6Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8F6Z contains 77 α-helices and 90 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, 15 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
β-strand	139-148	10	2
β-strand	156-160	5	1
β-strand	166	1	1
α-helix	170	1
β-strand	171	1	1
α-helix	172	1
β-strand	176-188	13	2
α-helix	197	1
β-strand	198-209	12	2
α-helix	213-214	2
α-helix	215-219	5
α-helix	220-234	15
α-helix	237-239	3
α-helix	242-261	20
α-helix	273-299	27
α-helix	310-316	7
α-helix	321-323	3
β-strand	329	1	3
α-helix	372-425	54

Chain B: 15 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	51-68	18	4
β-strand	80-82	3	4
β-strand	92-94	3	5
β-strand	97	1	4
α-helix	108-109	2
β-strand	110-112	3	4
β-strand	115-120	6	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	251-253	3
α-helix	256-275	20
α-helix	287-313	27
α-helix	324-327	4
α-helix	328-333	6
α-helix	334-337	4
α-helix	417-477	61

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	174-175	2	8
α-helix	177-179	3
β-strand	181	1	8
β-strand	186-190	5	9
β-strand	192	1	11
β-strand	193-198	6	9
β-strand	201-215	15	9
α-helix	218-220	3
α-helix	221-225	5
α-helix	226-237	12
α-helix	238-240	3
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	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	77-80	4	13
α-helix	82-84	3
β-strand	90-92	3	14
β-strand	95	1	13
β-strand	108-111	4	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	220-229	10
α-helix	230-234	5
α-helix	237-239	3
α-helix	242-261	20
α-helix	273-299	27
α-helix	310-314	5
α-helix	315-319	5
α-helix	320-322	3
β-strand	329	1	12
α-helix	372-425	54

Chain E: 12 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	3-12	10
β-strand	29-44	16	15
β-strand	49-66	18	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
α-helix	106	1
β-strand	107-111	5	15
β-strand	113-118	6	15
β-strand	121-127	7	15
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	1	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	237-242	6
α-helix	251-270	20
α-helix	282-308	27
β-strand	315	1	3
α-helix	319-327	9
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

>8F6Z_1 Acetylcholine receptor subunit alpha (chains A, D)
SEHETRLVANLLENYNKVIRPVEHHTHFVDITVGLQLIQLISVDEVNQIVETNVRLRQQW
IDVRLRWNPADYGGIKKIRLPSDDVWLPDLVLYNNADGDFAIVHMTKLLLDYTGKIMWTP
PAIFKSYCEIIVTHFPFDQQNCTMKLGIWTYDGTKVSISPESDRPDLSTFMESGEWVMKD
YRGWKHWVYYTCCPDTPYLDITYHFIMQRIPLYFVVNVIIPCLLFSFLTGLVFYLPTDSG
EKMTLSISVLLSLTVFLLVIVELIPSTSSAVPLIGKYMLFTMIFVISSIIITVVVINTHH
RSPSTHTMPQWVRKIFIDTIPNVMFFSTMKRASKEKQENKIFADDIDISDISGKQVTGEV
IFQTPLIKNPDVKSAIEGVKYIAEHMKSDEESSNAAEEWKYVAMVIDHILLCVFMLICII
GTVSVFAGRLIEL

Sequence of entity 2 (B), FASTA

>8F6Z_2 Acetylcholine receptor subunit delta (chains B)
VNEEERLINDLLIVNKYNKHVRPVKHNNEVVNIALSLTLSNLISLKETDETLTSNVWMDH
AWYDHRLTWNASEYSDISILRLPPELVWIPDIVLQNNNDGQYHVAYFCNVLVRPNGYVTW
LPPAIFRSSCPINVLYFPFDWQNCSLKFTALNYDANEITMDLMTDTIDGKDYPIEWIIID
PEAFTENGEWEIIHKPAKKNIYPDKFPNGTNYQDVTFYLIIRRKPLFYVINFITPCVLIS
FLASLAFYLPAESGEKMSTAISVLLAQAVFLLLTSQRLPETALAVPLIGKYLMFIMSLVT
GVIVNCGIVLNFHFRTPSTHVLSTRVKQIFLEKLPRILHMSRADESEQPDWQNDLKLRRS
SSVGYISKAQEYFNIKSRSELMFEKQSERHGLVPRVTPRIGFGNNNENIAASDQLHDEIK
SGIDSTNYIVKQIKEKNAYDEEVGNWNLVGQTIDRLSMFIITPVMVLGTIFIFVMGNFNH
PPAKPFEGDPFDYSSDHPRC

Sequence of entity 3 (C), FASTA

>8F6Z_3 Acetylcholine receptor subunit beta (chains C)
SVMEDTLLSVLFETYNPKVRPAQTVGDKVTVRVGLTLTNLLILNEKIEEMTTNVFLNLAW
TDYRLQWDPAAYEGIKDLRIPSSDVWQPDIVLMNNNDGSFEITLHVNVLVQHTGAVSWQP
SAIYRSSCTIKVMYFPFDWQNCTMVFKSYTYDTSEVTLQHALDAKGEREVKEIVINKDAF
TENGQWSIEHKPSRKNWRSDDPSYEDVTFYLIIQRKPLFYIVYTIIPCILISILAILVFY
LPPDAGEKMSLSISALLAVTVFLLLLADKVPETSLSVPIIIRYLMFIMILVAFSVILSVV
VLNLHHRSPNTHTMPNWIRQIFIETLPPFLWIQRPVTTPSPDSKPTIISRANDEYFIRKP
AGDFVCPVDNARVAVQPERLFSEMKWHLNGLTQPVTLPQDLKEAVEAIKYIAEQLESASE
FDDLKKDWQYVAMVADRLFLYVFFVICSIGTFSIFLDASHNVPPDNPFA

Sequence of entity 4 (E), FASTA

>8F6Z_4 Acetylcholine receptor subunit gamma (chains E)
ENEEGRLIEKLLGDYDKRIIPAKTLDHIIDVTLKLTLTNLISLNEKEEALTTNVWIEIQW
NDYRLSWNTSEYEGIDLVRIPSELLWLPDVVLENNVDGQFEVAYYANVLVYNDGSMYWLP
PAIYRSTCPIAVTYFPFDWQNCSLVFRSQTYNAHEVNLQLSAEEGEAVEWIHIDPEDFTE
NGEWTIRHRPAKKNYNWQLTKDDTDFQEIIFFLIIQRKPLFYIINIIAPCVLISSLVVLV
YFLPAQAGGQKCTLSISVLLAQTIFLFLIAQKVPETSLNVPLIGKYLIFVMFVSMLIVMN
CVIVLNVSLRTPNTHSLSEKIKHLFLGFLPKYLGMQLEPSEETPEKPQPRRRSSFGIMIK
AEEYILKKPRSELMFEEQKDRHGLKRVNKMTSDIDIGTTVDLYKDLANFAPEIKSCVEAC
NFIAKSTKEQNDSGSENENWVLIGKVIDKACFWIALLLFSIGTLAIFLTGHFNQVPEFPF
PGDPRKYVP

Ligands and cofactors

ID	Name	Formula	Copies
SCK	2,2'-[(1,4-dioxobutane-1,4-diyl)bis(oxy)]bis(n,n,n-trimethylethanaminium)	C14 H30 N2 O4	2
CLR	Cholesterol	C27 H46 O	3
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
POV	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl…	C42 H82 N O8 P	5
DD9	nonane	C9 H20	1

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
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,…
8F6Y 2.79 Å, Cryo-EM structure of Torpedo nicotinic acetylcholine receptor in complex with etomidate,…
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…

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