7Z14: Torpedo nicotinic acetylcholine receptor

Cryo-EM structure of Torpedo nicotinic acetylcholine receptor in complex with a short-chain neurotoxin. Determined by electron microscopy at 3.15 Å resolution. Released 17 Aug 2022.

Method: Electron microscopy
Resolution: 3.15 Å
Organisms: Tetronarce californica, synthetic construct
Chains: 7
Atoms: 15,856
Mol. weight: 286.87 kDa
Ligands: NAG
Released: 17 Aug 2022

Explore 7Z14 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7Z14 contains 60 α-helices and 109 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.

Chain A: 12 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	2-11	10
β-strand	29-34	6	1
β-strand	36	1	2
β-strand	37-44	8	3
β-strand	49-55	7	3
β-strand	57-61	5	1
α-helix	63-65	3
β-strand	77-78	2	1
α-helix	82-84	3
β-strand	90-92	3	4
β-strand	95	1	3
β-strand	109-111	3	1
β-strand	115-118	4	1
β-strand	121-127	7	3
β-strand	139-140	2	4
β-strand	143-148	6	4
β-strand	156-160	5	1
β-strand	166	1	2
β-strand	176-188	13	4
β-strand	198-209	12	4
α-helix	213-214	2
α-helix	215-219	5
α-helix	220-229	10
α-helix	232-234	3
α-helix	242-263	22
α-helix	273-299	27
α-helix	312-316	5
α-helix	321-323	3
α-helix	398-425	28

Chain B: 12 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	2-11	10
β-strand	29-42	14	5
β-strand	49-61	13	5
α-helix	69-71	3
β-strand	77-80	4	5
α-helix	82-84	3
β-strand	90-92	3	6
β-strand	95	1	5
α-helix	106-107	2
β-strand	108-111	4	5
β-strand	115-118	4	5
β-strand	121-127	7	5
β-strand	139-140	2	7
β-strand	145-148	4	6
β-strand	156-160	5	5
β-strand	162	1	8
β-strand	169	1	8
β-strand	172	1	9
β-strand	174	1	5
β-strand	181	1	5
β-strand	186-190	5	7
β-strand	192	1	9
β-strand	193-196	4	6
β-strand	206-209	4	6
β-strand	212-215	4	7
α-helix	218-220	3
α-helix	221-225	5
α-helix	226-240	15
α-helix	243-245	3
α-helix	248-269	22
α-helix	279-306	28
α-helix	316-322	7
α-helix	425-459	35

Chain C: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	3-8	6
α-helix	9-14	6
β-strand	31-44	14	10
β-strand	51-63	13	10
β-strand	80-82	3	10
α-helix	84-86	3
β-strand	93-94	2	11
α-helix	108-109	2
β-strand	110-112	3	10
β-strand	117-120	4	10
β-strand	123-129	7	10
β-strand	141-143	3	12
β-strand	146-149	4	11
β-strand	158-162	5	10
β-strand	164-166	3	13
β-strand	171-173	3	13
β-strand	176	1	14
β-strand	178	1	10
β-strand	190-194	5	12
β-strand	196	1	14
β-strand	197-201	5	11
β-strand	213-217	5	11
β-strand	220-223	4	12
α-helix	227-228	2
α-helix	229-233	5
α-helix	234-245	12
α-helix	246-248	3
α-helix	256-275	20
α-helix	287-313	27
α-helix	443-475	33

Chain D: 10 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	2-11	10
β-strand	29-44	16	15
β-strand	49-61	13	15
α-helix	69-72	4
β-strand	77-78	2	15
α-helix	82-84	3
β-strand	90-92	3	16
β-strand	95	1	15
β-strand	109-111	3	15
β-strand	115-118	4	15
β-strand	121-127	7	15
β-strand	139-140	2	16
β-strand	143-148	6	16
β-strand	156-160	5	15
β-strand	166	1	15
β-strand	176-190	15	16
β-strand	193-209	17	16
α-helix	213-214	2
α-helix	215-219	5
α-helix	220-229	10
α-helix	232-234	3
α-helix	242-263	22
α-helix	273-299	27
α-helix	400-424	25

Chain E: 13 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	3-12	10
β-strand	29-34	6	17
β-strand	36-44	9	18
β-strand	49-55	7	18
β-strand	57-59	3	17
β-strand	61	1	19
α-helix	63-65	3
α-helix	69-71	3
β-strand	78-80	3	17
α-helix	82-84	3
β-strand	90-92	3	20
β-strand	95	1	18
α-helix	106-107	2
β-strand	108-110	3	17
β-strand	115	1	19
β-strand	116-118	3	17
β-strand	121-127	7	18
α-helix	132-134	3
β-strand	139-142	4	21
β-strand	145-148	4	20
β-strand	156-160	5	17
β-strand	162-163	2	22
β-strand	166-167	2	22
β-strand	170	1	23
β-strand	172-173	2	18
β-strand	184-188	5	21
β-strand	190	1	23
β-strand	191-195	5	20
β-strand	207-211	5	20
β-strand	213-217	5	21
α-helix	220-222	3
α-helix	223-227	5
α-helix	228-234	7
α-helix	235-241	7
α-helix	252-270	19
α-helix	282-308	27
α-helix	441-472	32

Chain F: 1 helix, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	24
β-strand	7	1	25
α-helix	10-12	3
β-strand	14-16	3	24
β-strand	22-28	7	25
β-strand	33-39	7	25
β-strand	49-50	2	25
β-strand	53	1	25

Chain G: 1 helix, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	26
β-strand	7	1	27
α-helix	11-12	2
β-strand	14-16	3	26
β-strand	22-28	7	27
β-strand	33-39	7	27
β-strand	49	1	27
β-strand	53	1	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Acetylcholine receptor subunit alpha	A, D	protein	437	Tetronarce californica	P02710 (AlphaFold model)
Acetylcholine receptor subunit beta	B	protein	469	Tetronarce californica	P02712 (AlphaFold model)
Acetylcholine receptor subunit delta	C	protein	501	Tetronarce californica	P02718 (AlphaFold model)
Acetylcholine receptor subunit gamma	E	protein	489	Tetronarce californica	P02714 (AlphaFold model)
Consensus short-chain short-chain alpha-neurotoxin ScNtx	F, G	protein	60	synthetic construct

Sequence of entity 1 (A, D), FASTA

>7Z14_1 Acetylcholine receptor subunit alpha (chains A, D)
SEHETRLVANLLENYNKVIRPVEHHTHFVDITVGLQLIQLISVDEVNQIVETNVRLRQQW
IDVRLRWNPADYGGIKKIRLPSDDVWLPDLVLYNNADGDFAIVHMTKLLLDYTGKIMWTP
PAIFKSYCEIIVTHFPFDQQNCTMKLGIWTYDGTKVSISPESDRPDLSTFMESGEWVMKD
YRGWKHWVYYTCCPDTPYLDITYHFIMQRIPLYFVVNVIIPCLLFSFLTGLVFYLPTDSG
EKMTLSISVLLSLTVFLLVIVELIPSTSSAVPLIGKYMLFTMIFVISSIIITVVVINTHH
RSPSTHTMPQWVRKIFIDTIPNVMFFSTMKRASKEKQENKIFADDIDISDISGKQVTGEV
IFQTPLIKNPDVKSAIEGVKYIAEHMKSDEESSNAAEEWKYVAMVIDHILLCVFMLICII
GTVSVFAGRLIELSQEG

Sequence of entity 2 (B), FASTA

>7Z14_2 Acetylcholine receptor subunit beta (chains B)
SVMEDTLLSVLFETYNPKVRPAQTVGDKVTVRVGLTLTNLLILNEKIEEMTTNVFLNLAW
TDYRLQWDPAAYEGIKDLRIPSSDVWQPDIVLMNNNDGSFEITLHVNVLVQHTGAVSWQP
SAIYRSSCTIKVMYFPFDWQNCTMVFKSYTYDTSEVTLQHALDAKGEREVKEIVINKDAF
TENGQWSIEHKPSRKNWRSDDPSYEDVTFYLIIQRKPLFYIVYTIIPCILISILAILVFY
LPPDAGEKMSLSISALLAVTVFLLLLADKVPETSLSVPIIIRYLMFIMILVAFSVILSVV
VLNLHHRSPNTHTMPNWIRQIFIETLPPFLWIQRPVTTPSPDSKPTIISRANDEYFIRKP
AGDFVCPVDNARVAVQPERLFSEMKWHLNGLTQPVTLPQDLKEAVEAIKYIAEQLESASE
FDDLKKDWQYVAMVADRLFLYVFFVICSIGTFSIFLDASHNVPPDNPFA

Sequence of entity 3 (C), FASTA

>7Z14_3 Acetylcholine receptor subunit delta (chains C)
VNEEERLINDLLIVNKYNKHVRPVKHNNEVVNIALSLTLSNLISLKETDETLTSNVWMDH
AWYDHRLTWNASEYSDISILRLPPELVWIPDIVLQNNNDGQYHVAYFCNVLVRPNGYVTW
LPPAIFRSSCPINVLYFPFDWQNCSLKFTALNYDANEITMDLMTDTIDGKDYPIEWIIID
PEAFTENGEWEIIHKPAKKNIYPDKFPNGTNYQDVTFYLIIRRKPLFYVINFITPCVLIS
FLASLAFYLPAESGEKMSTAISVLLAQAVFLLLTSQRLPETALAVPLIGKYLMFIMSLVT
GVIVNCGIVLNFHFRTPSTHVLSTRVKQIFLEKLPRILHMSRADESEQPDWQNDLKLRRS
SSVGYISKAQEYFNIKSRSELMFEKQSERHGLVPRVTPRIGFGNNNENIAASDQLHDEIK
SGIDSTNYIVKQIKEKNAYDEEVGNWNLVGQTIDRLSMFIITPVMVLGTIFIFVMGNFNH
PPAKPFEGDPFDYSSDHPRCA

Sequence of entity 4 (E), FASTA

>7Z14_4 Acetylcholine receptor subunit gamma (chains E)
ENEEGRLIEKLLGDYDKRIIPAKTLDHIIDVTLKLTLTNLISLNEKEEALTTNVWIEIQW
NDYRLSWNTSEYEGIDLVRIPSELLWLPDVVLENNVDGQFEVAYYANVLVYNDGSMYWLP
PAIYRSTCPIAVTYFPFDWQNCSLVFRSQTYNAHEVNLQLSAEEGEAVEWIHIDPEDFTE
NGEWTIRHRPAKKNYNWQLTKDDTDFQEIIFFLIIQRKPLFYIINIIAPCVLISSLVVLV
YFLPAQAGGQKCTLSISVLLAQTIFLFLIAQKVPETSLNVPLIGKYLIFVMFVSMLIVMN
CVIVLNVSLRTPNTHSLSEKIKHLFLGFLPKYLGMQLEPSEETPEKPQPRRRSSFGIMIK
AEEYILKKPRSELMFEEQKDRHGLKRVNKMTSDIDIGTTVDLYKDLANFAPEIKSCVEAC
NFIAKSTKEQNDSGSENENWVLIGKVIDKACFWIALLLFSIGTLAIFLTGHFNQVPEFPF
PGDPRKYVP

Sequence of entity 5 (F, G), FASTA

>7Z14_5 Consensus short-chain short-chain alpha-neurotoxin ScNtx (chains F, G)
MICYNQQSSQPPTTKTCSETSCYKKTWRDHRGTIIERGCGCPKVKPGIKLHCCRTDKCNN

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

The molecular mechanism of snake short-chain alpha-neurotoxin binding to muscle-type nicotinic acetylcholine receptors. Nys, M., Zarkadas, E., Brams, M. et al. Nat Commun (2022) 13:4543-4543. DOI 10.1038/s41467-022-32174-7 · 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,…
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…

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