9DMG: Human muscle nAChR apo state

Human muscle nAChR apo state. Determined by electron microscopy at 2.05 Å resolution. Released 9 Apr 2025.

Method: Electron microscopy
Resolution: 2.05 Å
Organism: Homo sapiens
Chains: 5
Atoms: 17,223
Mol. weight: 285.71 kDa
Ligands: POV, CLR, MAN
Released: 9 Apr 2025

Explore 9DMG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9DMG contains 85 α-helices and 83 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	69-72	4
β-strand	77-80	4	1
α-helix	82-84	3
β-strand	90-92	3	2
β-strand	95	1	1
β-strand	101	1	2
α-helix	106-107	2
β-strand	108-111	4	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	170-173	4
β-strand	176-190	15	2
β-strand	193-209	17	2
α-helix	212-214	3
α-helix	215-219	5
α-helix	220-230	11
α-helix	231-234	4
α-helix	237-239	3
α-helix	242-263	22
α-helix	273-299	27
α-helix	310-312	3
α-helix	313-319	7
α-helix	320-323	4
α-helix	370-434	65

Chain B: 18 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	3-12	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
α-helix	106-107	2
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	162	1	15
β-strand	168	1	15
β-strand	171	1	16
β-strand	173	1	13
β-strand	185-189	5	14
β-strand	191	1	16
β-strand	192-197	6	14
β-strand	207-218	12	14
α-helix	221-223	3
α-helix	224-228	5
α-helix	229-236	8
α-helix	237-243	7
α-helix	252-271	20
α-helix	283-309	27
β-strand	316	1	5
α-helix	320-323	4
α-helix	324-329	6
α-helix	330-333	4
α-helix	398	1
α-helix	399-403	5
α-helix	404-458	55
α-helix	461-463	3

Chain C: 16 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	2-11	10
β-strand	29-44	16	3
β-strand	49-61	13	3
α-helix	69-72	4
β-strand	77-80	4	3
α-helix	82-84	3
β-strand	90-92	3	4
β-strand	95	1	3
β-strand	101	1	4
α-helix	106-107	2
β-strand	108-111	4	3
β-strand	115-118	4	3
β-strand	121-127	7	3
β-strand	139-148	10	4
β-strand	156-160	5	3
β-strand	166	1	3
α-helix	170-173	4
β-strand	176-188	13	4
β-strand	198-209	12	4
α-helix	212-214	3
α-helix	215-219	5
α-helix	220-230	11
α-helix	231-234	4
α-helix	237-239	3
α-helix	242-263	22
α-helix	273-299	27
α-helix	310-312	3
α-helix	313-319	7
α-helix	320-323	4
β-strand	328	1	5
α-helix	370-434	65

Chain D: 19 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	2-8	7
α-helix	9-14	6
β-strand	31-46	16	9
β-strand	51-63	13	9
α-helix	65-67	3
α-helix	71-74	4
β-strand	79-82	4	9
α-helix	84-86	3
β-strand	93-94	2	10
β-strand	97	1	9
α-helix	108-109	2
β-strand	110-113	4	9
β-strand	117-120	4	9
β-strand	123-129	7	9
β-strand	141-149	9	10
β-strand	158-162	5	9
β-strand	164-167	4	11
β-strand	170-173	4	11
β-strand	176	1	12
β-strand	178	1	9
α-helix	184-187	4
β-strand	190-194	5	10
β-strand	196	1	12
β-strand	197-201	5	10
β-strand	213-223	11	10
α-helix	226-228	3
α-helix	229-233	5
α-helix	234-242	9
α-helix	243-247	5
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	340-343	4
α-helix	409-472	64

Chain E: 16 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	2-11	10
α-helix	27-28	2
β-strand	29-44	16	6
β-strand	49-66	18	6
α-helix	69-72	4
β-strand	77-81	5	6
α-helix	82-84	3
β-strand	90-92	3	7
β-strand	95	1	6
β-strand	107-111	5	6
β-strand	113-118	6	6
β-strand	121-127	7	6
β-strand	139-148	10	7
β-strand	156-160	5	6
β-strand	171	1	8
β-strand	173	1	6
β-strand	180	1	6
β-strand	185-189	5	7
β-strand	191	1	8
β-strand	192-195	4	7
α-helix	196-197	2
β-strand	211-220	10	7
α-helix	223-225	3
α-helix	226-230	5
α-helix	231-242	12
α-helix	243-245	3
α-helix	248-250	3
α-helix	253-272	20
α-helix	284-310	27
α-helix	321-324	4
α-helix	325-330	6
α-helix	331-334	4
α-helix	408-468	61

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Acetylcholine receptor subunit alpha	A, C	protein	457	Homo sapiens	P02708 (AlphaFold model)
Acetylcholine receptor subunit beta	E	protein	503	Homo sapiens	P11230 (AlphaFold model)
Acetylcholine receptor subunit delta	D	protein	517	Homo sapiens	Q07001 (AlphaFold model)
Acetylcholine receptor subunit epsilon	B	protein	493	Homo sapiens	Q04844 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>9DMG_1 Acetylcholine receptor subunit alpha (chains A, C)
MEPWPLLLLFSLCSAGLVLGSEHETRLVAKLFKDYSSVVRPVEDHRQVVEVTVGLQLIQL
INVDEVNQIVTTNVRLKQQWVDYNLKWNPDDYGGVKKIHIPSEKIWRPDLVLYNNADGDF
AIVKFTKVLLQYTGHITWTPPAIFKSYCEIIVTHFPFDEQNCSMKLGTWTYDGSVVAINP
ESDQPDLSNFMESGEWVIKESRGWKHSVTYSCCPDTPYLDITYHFVMQRLPLYFIVNVII
PCLLFSFLTGLVFYLPTDSGEKMTLSISVLLSLTVFLLVIVELIPSTSSAVPLIGKYMLF
TMVFVIASIIITVIVINTHHRSPSTHVMPNWVRKVFIDTIPNIMFFSTMKRPSREKQDKK
IFTEDIDISDISGKPGPPPMGFHSPLIKHPEVKSAIEGIKYIAETMKSDQESNNAAAEWK
YVAMVMDHILLGVFMLVCIIGTLAVFAGRLIELNQQG

Sequence of entity 2 (E), FASTA

>9DMG_2 Acetylcholine receptor subunit beta (chains E)
MTPGALLMLLGALGAPLAPGVRGSEAEGRLREKLFSGYDSSVRPAREVGDRVRVSVGLIL
AQLISLNEKDEEMSTKVYLDLEWTDYRLSWDPAEHDGIDSLRITAESVWLPDVVLLNNND
GNFDVALDISVVVSSDGSVRWQPPGIYRSSCSIQVTYFPFDWQNCTMVFSSYSYDSSEVS
LQTGLGPDGQGHQEIHIHEGTFIENGQWEIIHKPSRLIQPPGDPRGGREGQRQEVIFYLI
IRRKPLFYLVNVIAPCILITLLAIFVFYLPPDAGEKMGLSIFALLTLTVFLLLLADKVPE
TSLSVPIIIKYLMFTMVLVTFSVILSVVVLNLHHRSPHTHQMPLWVRQIFIHKLPLYLRL
KRPKPERDLMPEPPHCSSPGSGWGRGTDEYFIRKPPSDFLFPKPNRFQPELSAPDLRRFI
DGPNRAVALLPELREVVSSISYIARQLQEQEDHDALKEDWQFVAMVVDRLFLWTFIIFTS
VGTLVIFLDATYHLPPPDPFPSR

Sequence of entity 3 (D), FASTA

>9DMG_3 Acetylcholine receptor subunit delta (chains D)
MEGPVLTLGLLAALAVCGSWGLNEEERLIRHLFQEKGYNKELRPVAHKEESVDVALALTL
SNLISLKEVEETLTTNVWIEHGWTDNRLKWNAEEFGNISVLRLPPDMVWLPEIVLENNND
GSFQISYSCNVLVYHYGFVYWLPPAIFRSSCPISVTYFPFDWQNCSLKFSSLKYTAKEIT
LSLKQDAKENRTYPVEWIIIDPEGFTENGEWEIVHRPARVNVDPRAPLDSPSRQDITFYL
IIRRKPLFYIINILVPCVLISFMVNLVFYLPADSGEKTSVAISVLLAQSVFLLLISKRLP
ATSMAIPLIGKFLLFGMVLVTMVVVICVIVLNIHFRTPSTHVLSEGVKKLFLETLPELLH
MSRPAEDGPSPGALVRRSSSLGYISKAEEYFLLKSRSDLMFEKQSERHGLARRLTTARRP
PASSEQAQQELFNELKPAVDGANFIVNHMRDQNNYNEEKDSWNRVARTVDRLCLFVVTPV
MVVGTAWIFLQGVYNQPPPQPFPGDPYSYNVQDKRFI

Sequence of entity 4 (B), FASTA

>9DMG_4 Acetylcholine receptor subunit epsilon (chains B)
MARAPLGVLLLLGLLGRGVGKNEELRLYHHLFNNYDPGSRPVREPEDTVTISLKVTLTNL
ISLNEKEETLTTSVWIGIDWQDYRLNYSKDDFGGIETLRVPSELVWLPEIVLENNIDGQF
GVAYDANVLVYEGGSVTWLPPAIYRSVCAVEVTYFPFDWQNCSLIFRSQTYNAEEVEFTF
AVDNDGKTINKIDIDTEAYTENGEWAIDFCPGVIRRHHGGATDGPGETDVIYSLIIRRKP
LFYVINIIVPCVLISGLVLLAYFLPAQAGGQKCTVSINVLLAQTVFLFLIAQKIPETSLS
VPLLGRFLIFVMVVATLIVMNCVIVLNVSQRTPTTHAMSPRLRHVLLELLPRLLGSPPPP
EAPRAASPPRRASSVGLLLRAEELILKKPRSELVFEGQRHRQGTWTAAFCQSLGAAAPEV
RCCVDAVNFVAESTRDQEATGEEVSDWVRMGNALDNICFWAALVLFSVGSSLIFLGAYFN
RVPDLPYAPCIQP

Ligands and cofactors

ID	Name	Formula	Copies
POV	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl…	C42 H82 N O8 P	4
CLR	Cholesterol	C27 H46 O	7
MAN	alpha-D-mannopyranose	C6 H12 O6	1

Primary citation

Autoimmune mechanisms elucidated through muscle acetylcholine receptor structures. Li, H., Pham, M.C., Teng, J. et al. Cell (2025) 188:2390-2406.e20. DOI 10.1016/j.cell.2025.03.004 · PubMed

Other PDB entries of the same protein (UniProt P02708 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9DMS 1.92 Å, Human muscle nAChR with fab6-bound
9DMH 2.06 Å, Human muscle nAChR ACh-bound state
9DMQ 2.06 Å, Human muscle nAChR with fab3-bound
9DMV 2.13 Å, Human muscle nAChR with fab9-bound
9DMT 2.18 Å, Human muscle nAChR with fab7-bound
9DMJ 2.19 Å, Human muscle nAChR with two fab1b-bound
9YER 2.19 Å, Human muscle nAChR SCCMS eT264P ACh bound
9YE8 2.22 Å, Human muscle nAChR SCCMS eL269F ACh bound
4ZJS 2.23 Å, Crystal structure of a chimeric acetylcholine binding protein from Aplysia Californica…
9DML 2.24 Å, Human muscle nAChR with fab2-bound
9YEI 2.36 Å, Human muscle nAChR SCCMS eL269F ACh, Reboxetine bound (lower 1)
9YET 2.36 Å, Human muscle nAChR SCCMS eT264P ACh, Reboxetine bound

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