9DML: Human muscle nAChR with fab2-bound

Human muscle nAChR with fab2-bound. Determined by electron microscopy at 2.24 Å resolution. Released 9 Apr 2025.

Method: Electron microscopy
Resolution: 2.24 Å
Organism: Homo sapiens
Chains: 9
Atoms: 23,688
Mol. weight: 392.27 kDa
Ligands: NAG, CLR, POV
Released: 9 Apr 2025

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

Secondary structure: helices and β-sheets

9DML contains 102 α-helices and 171 β-strands across 9 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: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	34-38	5	1
β-strand	42-43	2	2
α-helix	48	1
β-strand	49-56	8	1
β-strand	65-73	9	3
β-strand	77-84	8	3
β-strand	90-92	3	3
β-strand	100-105	6	1
β-strand	110-115	6	1
α-helix	120-122	3
β-strand	124-138	15	3
β-strand	142-152	11	3
β-strand	156-158	3	3
β-strand	159-160	2	2
α-helix	163-165	3
β-strand	166	1	4
β-strand	169-173	5	5
β-strand	184-194	11	5
β-strand	195	1	4
β-strand	199-203	5	6
β-strand	213-214	2	5
α-helix	215-217	3
β-strand	218-219	2	5
β-strand	225-234	10	5
α-helix	235-237	3
β-strand	243-249	7	6
β-strand	254-260	7	6

Chain B: 2 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	34-38	5	7
β-strand	42-43	2	8
β-strand	49-56	8	7
β-strand	65-73	9	9
β-strand	77-84	8	9
β-strand	90-92	3	9
β-strand	100-105	6	7
β-strand	110-115	6	7
α-helix	120-122	3
β-strand	124-138	15	9
β-strand	142-152	11	9
β-strand	156-158	3	9
β-strand	159-160	2	8
β-strand	166	1	10
β-strand	169-173	5	11
β-strand	184-194	11	11
β-strand	195	1	10
β-strand	199-203	5	12
β-strand	208	1	12
β-strand	212-214	3	11
α-helix	215-217	3
β-strand	218-219	2	11
β-strand	225-234	10	11
β-strand	243-249	7	12
β-strand	254-260	7	12

Chain C: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	23-26	4	13
β-strand	29-32	4	14
β-strand	38-44	7	13
β-strand	52-57	6	14
β-strand	64-68	5	14
β-strand	72-73	2	14
α-helix	74	1
β-strand	81-85	5	13
β-strand	89-94	6	13
α-helix	99-101	3
β-strand	104-110	7	14
β-strand	116-118	3	14
α-helix	119-121	3
β-strand	122-126	5	14
β-strand	131	1	15
β-strand	134-138	5	16
α-helix	139-141	3
α-helix	142-146	5
β-strand	149-159	11	16
β-strand	160	1	15
β-strand	164-170	7	17
β-strand	174	1	17
β-strand	179-183	5	16
α-helix	184-187	4
β-strand	193-202	10	16
α-helix	203-208	6
β-strand	211-218	8	17
β-strand	225-230	6	17

Chain D: 5 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	23-26	4	18
β-strand	29-32	4	19
β-strand	38-44	7	18
β-strand	52-57	6	19
β-strand	64-68	5	19
β-strand	72-73	2	19
α-helix	74	1
β-strand	81-84	4	18
β-strand	89-94	6	18
α-helix	99-101	3
β-strand	104-109	6	19
β-strand	117-118	2	19
β-strand	122-126	5	19
β-strand	131	1	20
α-helix	132-133	2
β-strand	134-138	5	21
α-helix	142-146	5
β-strand	149-159	11	21
β-strand	160	1	20
β-strand	164-170	7	22
β-strand	173-175	3	22
β-strand	179-183	5	21
β-strand	193-202	10	21
α-helix	203-208	6
β-strand	212-218	7	22
β-strand	225-229	5	22

Chain E: 17 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	2-11	10
β-strand	27-28	2	9
β-strand	29-44	16	23
β-strand	49-61	13	23
α-helix	69-72	4
β-strand	77-80	4	23
α-helix	82-84	3
β-strand	90-92	3	24
β-strand	95	1	23
β-strand	101	1	24
α-helix	106-107	2
β-strand	108-111	4	23
β-strand	115-118	4	23
β-strand	121-127	7	23
α-helix	129-131	3
β-strand	139-148	10	24
β-strand	156-160	5	23
β-strand	166	1	23
α-helix	170-173	4
β-strand	176-190	15	24
β-strand	193-209	17	24
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	242-263	22
α-helix	273-299	27
α-helix	310-312	3
α-helix	313-319	7
α-helix	320-322	3
α-helix	370-435	66

Chain F: 15 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	2-11	10
β-strand	27-28	2	3
β-strand	29-44	16	25
β-strand	49-61	13	25
α-helix	69-72	4
β-strand	77-81	5	25
α-helix	82-84	3
β-strand	90-92	3	26
β-strand	95	1	25
β-strand	101	1	26
α-helix	106	1
β-strand	107-111	5	25
β-strand	115-118	4	25
β-strand	121-127	7	25
β-strand	139-142	4	26
β-strand	145-148	4	26
β-strand	156-160	5	25
β-strand	166	1	25
α-helix	170-173	4
β-strand	176-188	13	26
β-strand	198-209	12	26
α-helix	212-214	3
α-helix	215-219	5
α-helix	220-229	10
α-helix	230-234	5
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 G: 17 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	2-11	10
α-helix	27-28	2
β-strand	29-44	16	27
β-strand	49-66	18	27
α-helix	69-72	4
β-strand	77-81	5	27
α-helix	82-84	3
β-strand	90-92	3	28
β-strand	95	1	27
β-strand	107-111	5	27
β-strand	113-118	6	27
β-strand	121-127	7	27
β-strand	139-148	10	28
β-strand	156-160	5	27
β-strand	171	1	29
β-strand	173	1	27
β-strand	180	1	27
β-strand	185-189	5	28
β-strand	191	1	29
β-strand	192-195	4	28
α-helix	196-198	3
β-strand	211-220	10	28
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	253-271	19
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
α-helix	471-473	3

Chain H: 17 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	2-8	7
α-helix	9-14	6
β-strand	31-46	16	30
β-strand	51-63	13	30
α-helix	65-67	3
α-helix	72-74	3
β-strand	79-82	4	30
α-helix	84-86	3
β-strand	93-94	2	31
β-strand	97	1	30
β-strand	110-113	4	30
β-strand	117-120	4	30
β-strand	123-129	7	30
β-strand	141-149	9	31
β-strand	158-162	5	30
β-strand	164-167	4	32
β-strand	170-173	4	32
β-strand	176	1	33
β-strand	178	1	30
β-strand	190-194	5	31
β-strand	196	1	33
β-strand	197-201	5	31
β-strand	213-223	11	31
α-helix	226-228	3
α-helix	229-233	5
α-helix	234-241	8
α-helix	242-248	7
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

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab2 heavy chain	A, B	protein	273	Homo sapiens
Fab2 light chain	C, D	protein	234	Homo sapiens
Acetylcholine receptor subunit alpha	E, F	protein	457	Homo sapiens	P02708 (AlphaFold model)
Acetylcholine receptor subunit beta	G	protein	503	Homo sapiens	P11230 (AlphaFold model)
Acetylcholine receptor subunit delta	H	protein	517	Homo sapiens	Q07001 (AlphaFold model)
Acetylcholine receptor subunit epsilon	I	protein	493	Homo sapiens	Q04844 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9DML_1 Fab2 heavy chain (chains A, B)
MDSKGSSQKGSRLLLLLVVSNLLLCQGVVSAQVQLQESGPGLVKPSETLSLTCTLSDGSI
SVSTYYWGWVRQSPEKGLEWIASIYYTGDSYYNPSLKSRVTISLDKSKNQFSLRLRSVTA
ADTAVYFCARDHRRSFWGSGSGYNYRYYFDMWGQGTLVTVSSASTKGPSVFPLAPSSKST
SGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGT
QTYICNVNHKPSNTKVDKKVEPKSCGSHHHHHH

Sequence of entity 2 (C, D), FASTA

>9DML_2 Fab2 light chain (chains C, D)
MGWSCIILFLVATATGVHSDIQMTQSPSLLPASVGERVTITCQASQDINNYLNWYQQKPG
KAPKLLIYDASKLETGVPSRFSGSGSGTDFNLTISSLQPEDFATYYCHQYGNLPVHTFGQ
GTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQ
ESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (E, F), FASTA

>9DML_3 Acetylcholine receptor subunit alpha (chains E, F)
MEPWPLLLLFSLCSAGLVLGSEHETRLVAKLFKDYSSVVRPVEDHRQVVEVTVGLQLIQL
INVDEVNQIVTTNVRLKQQWVDYNLKWNPDDYGGVKKIHIPSEKIWRPDLVLYNNADGDF
AIVKFTKVLLQYTGHITWTPPAIFKSYCEIIVTHFPFDEQNCSMKLGTWTYDGSVVAINP
ESDQPDLSNFMESGEWVIKESRGWKHSVTYSCCPDTPYLDITYHFVMQRLPLYFIVNVII
PCLLFSFLTGLVFYLPTDSGEKMTLSISVLLSLTVFLLVIVELIPSTSSAVPLIGKYMLF
TMVFVIASIIITVIVINTHHRSPSTHVMPNWVRKVFIDTIPNIMFFSTMKRPSREKQDKK
IFTEDIDISDISGKPGPPPMGFHSPLIKHPEVKSAIEGIKYIAETMKSDQESNNAAAEWK
YVAMVMDHILLGVFMLVCIIGTLAVFAGRLIELNQQG

Sequence of entity 4 (G), FASTA

>9DML_4 Acetylcholine receptor subunit beta (chains G)
MTPGALLMLLGALGAPLAPGVRGSEAEGRLREKLFSGYDSSVRPAREVGDRVRVSVGLIL
AQLISLNEKDEEMSTKVYLDLEWTDYRLSWDPAEHDGIDSLRITAESVWLPDVVLLNNND
GNFDVALDISVVVSSDGSVRWQPPGIYRSSCSIQVTYFPFDWQNCTMVFSSYSYDSSEVS
LQTGLGPDGQGHQEIHIHEGTFIENGQWEIIHKPSRLIQPPGDPRGGREGQRQEVIFYLI
IRRKPLFYLVNVIAPCILITLLAIFVFYLPPDAGEKMGLSIFALLTLTVFLLLLADKVPE
TSLSVPIIIKYLMFTMVLVTFSVILSVVVLNLHHRSPHTHQMPLWVRQIFIHKLPLYLRL
KRPKPERDLMPEPPHCSSPGSGWGRGTDEYFIRKPPSDFLFPKPNRFQPELSAPDLRRFI
DGPNRAVALLPELREVVSSISYIARQLQEQEDHDALKEDWQFVAMVVDRLFLWTFIIFTS
VGTLVIFLDATYHLPPPDPFPSR

Sequence of entity 5 (H), FASTA

>9DML_5 Acetylcholine receptor subunit delta (chains H)
MEGPVLTLGLLAALAVCGSWGLNEEERLIRHLFQEKGYNKELRPVAHKEESVDVALALTL
SNLISLKEVEETLTTNVWIEHGWTDNRLKWNAEEFGNISVLRLPPDMVWLPEIVLENNND
GSFQISYSCNVLVYHYGFVYWLPPAIFRSSCPISVTYFPFDWQNCSLKFSSLKYTAKEIT
LSLKQDAKENRTYPVEWIIIDPEGFTENGEWEIVHRPARVNVDPRAPLDSPSRQDITFYL
IIRRKPLFYIINILVPCVLISFMVNLVFYLPADSGEKTSVAISVLLAQSVFLLLISKRLP
ATSMAIPLIGKFLLFGMVLVTMVVVICVIVLNIHFRTPSTHVLSEGVKKLFLETLPELLH
MSRPAEDGPSPGALVRRSSSLGYISKAEEYFLLKSRSDLMFEKQSERHGLARRLTTARRP
PASSEQAQQELFNELKPAVDGANFIVNHMRDQNNYNEEKDSWNRVARTVDRLCLFVVTPV
MVVGTAWIFLQGVYNQPPPQPFPGDPYSYNVQDKRFI

Sequence of entity 6 (I), FASTA

>9DML_6 Acetylcholine receptor subunit epsilon (chains I)
MARAPLGVLLLLGLLGRGVGKNEELRLYHHLFNNYDPGSRPVREPEDTVTISLKVTLTNL
ISLNEKEETLTTSVWIGIDWQDYRLNYSKDDFGGIETLRVPSELVWLPEIVLENNIDGQF
GVAYDANVLVYEGGSVTWLPPAIYRSVCAVEVTYFPFDWQNCSLIFRSQTYNAEEVEFTF
AVDNDGKTINKIDIDTEAYTENGEWAIDFCPGVIRRHHGGATDGPGETDVIYSLIIRRKP
LFYVINIIVPCVLISGLVLLAYFLPAQAGGQKCTVSINVLLAQTVFLFLIAQKIPETSLS
VPLLGRFLIFVMVVATLIVMNCVIVLNVSQRTPTTHAMSPRLRHVLLELLPRLLGSPPPP
EAPRAASPPRRASSVGLLLRAEELILKKPRSELVFEGQRHRQGTWTAAFCQSLGAAAPEV
RCCVDAVNFVAESTRDQEATGEEVSDWVRMGNALDNICFWAALVLFSVGSSLIFLGAYFN
RVPDLPYAPCIQP

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3
CLR	Cholesterol	C27 H46 O	2
POV	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl…	C42 H82 N O8 P	2

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
9DMG 2.05 Å, Human muscle nAChR apo state
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…
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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