9EJZ: Nanobody 35

Human M5 muscarinic acetylcholine receptor complex with mini-Gq, agonist acetylcholine and positive allosteric modulator VU6007678. Determined by electron microscopy at 2.06 Å resolution. Released 13 Aug 2025.

Method: Electron microscopy
Resolution: 2.06 Å
Organisms: Lama glama, Rattus norvegicus, Homo sapiens
Chains: 6
Atoms: 9,985
Mol. weight: 158.67 kDa
Ligands: ACH, A1BKS
Released: 13 Aug 2025

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

Secondary structure: helices and β-sheets

9EJZ contains 39 α-helices and 72 β-strands across 6 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: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	14-38	25
β-strand	40-47	8	11
β-strand	207-214	8	11
β-strand	217-224	8	11
α-helix	234-238	5
β-strand	243-249	7	11
α-helix	266-278	13
α-helix	280-282	3
β-strand	286-292	7	11
α-helix	294-303	10
α-helix	308-311	4
α-helix	313-315	3
α-helix	326-327	2
α-helix	332-351	20
β-strand	359-364	6	11
α-helix	371-390	20

Chain B: 3 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	3-24	22
α-helix	30-33	4
α-helix	38-39	2
β-strand	47-52	6	3
β-strand	58-63	6	4
β-strand	69-74	6	4
β-strand	78-83	6	4
β-strand	88-94	7	4
β-strand	100-102	3	5
β-strand	105	1	6
β-strand	111-114	4	6
β-strand	115-116	2	5
β-strand	121-125	5	6
β-strand	134-139	6	6
β-strand	146-151	6	7
β-strand	156-161	6	7
β-strand	165-170	6	7
β-strand	175-181	7	7
β-strand	187-192	6	8
β-strand	198-203	6	8
β-strand	207-212	6	8
β-strand	218-223	6	8
β-strand	229-234	6	9
β-strand	240-245	6	9
β-strand	250-254	5	9
β-strand	259-264	6	9
β-strand	273-278	6	10
β-strand	284-289	6	10
β-strand	294-298	5	10
β-strand	303-308	6	10
β-strand	315-320	6	3
β-strand	327-331	5	3
β-strand	335-339	5	3

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	7-21	15
α-helix	30-43	14
α-helix	53-55	3

Chain H: 6 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	12
β-strand	11-12	2	13
β-strand	18-25	8	12
α-helix	29-31	3
β-strand	33-39	7	14
β-strand	45-51	7	14
α-helix	53-55	3
β-strand	58-60	3	14
β-strand	68-73	6	12
β-strand	78-83	6	12
α-helix	88-90	3
β-strand	92-99	8	14
β-strand	111	1	14
β-strand	115-117	3	14
β-strand	118-119	2	13
β-strand	140-141	2	15
β-strand	146-149	4	16
β-strand	155-161	7	15
β-strand	166	1	17
β-strand	172	1	17
β-strand	174-179	6	16
β-strand	185-190	6	16
β-strand	194-195	2	16
α-helix	196	1
β-strand	203-207	5	15
β-strand	211-216	6	15
α-helix	221-223	3
β-strand	225-231	7	16
α-helix	237	1
β-strand	239	1	16
β-strand	243-247	5	16

Chain N: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	10-11	2	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-39	6	2
β-strand	45-51	7	2
β-strand	58-60	3	2
α-helix	62-64	3
β-strand	68-73	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-98	7	2
β-strand	118	1	2
β-strand	122-125	4	2

Chain R: 14 helices, 0 β-strands

Element	Residues	Length
α-helix	27-57	31
α-helix	65-78	14
α-helix	79-83	5
α-helix	84-93	10
α-helix	100-133	34
α-helix	137-139	3
α-helix	144-172	29
α-helix	191-198	8
α-helix	199-203	5
α-helix	204-231	28
α-helix	439-465	27
α-helix	474-491	18
α-helix	492-496	5
α-helix	500-510	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
nanobody 35	N	protein	156	Lama glama
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	350	Rattus norvegicus	P54311 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	68	Homo sapiens	P59768 (AlphaFold model)
Guanine nucleotide-binding protein Gq chimera	A	protein	245	Homo sapiens
scFv16	H	protein	259	Mus musculus
Human M5 muscarinic acetylcholine receptor	R	protein	343	Homo sapiens

Sequence of entity 1 (N), FASTA

>9EJZ_1 nanobody 35 (chains N)
MKYLLPTAAAGLLLLAAQPAMAQVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVR
QAPGKGLEWVSDISQSGASISYTGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCAR
CPAPFTRDCFDVTSTTYAYRGQGTQVTVSSHHHHHH

Sequence of entity 2 (B), FASTA

>9EJZ_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRT
LRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGN
YVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWD
IETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDIN
AICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYD
DFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (G), FASTA

>9EJZ_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFC

Sequence of entity 4 (A), FASTA

>9EJZ_4 Guanine nucleotide-binding protein Gq chimera (chains A)
GCTLSAEDKAAVERSKMIDRNLREDGEKARRTLRLLLLGADNSGKSTIVKQMRILHGGSG
GSGGTSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQEA
LNDFKSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEPG
EDPRVTRAKYFIRKEFVDISTASGDGRHICYPHFTCAVDTENARRIFNDCKDIILQMNLR
EYNLV

Sequence of entity 5 (H), FASTA

>9EJZ_5 scFv16 (chains H)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAAHHHHHHHH

Sequence of entity 6 (R), FASTA

>9EJZ_6 Human M5 muscarinic acetylcholine receptor (chains R)
DYKDDDDAEGDSYHNATTVNGTPVNHQPLERHRLWEVITIAAVTAVVSLITIVGNVLVMI
SFKVNSQLKTVNNYYLLSLACADLIIGIFSMNLYTTYILMGRWALGSLACDLWLALDYVA
SNASVMNLLVISFDRYFSITRPLTYRAKRTPKRAGIMIGLAWLISFILWAPAILCWQYLV
GKRTVPLDECQIQFLSEPTITFGTAIAAFYIPVSVMTILYCRIYRETEKRTKDLADLQGS
DSVPSHQMTKRKRVVLVKERKAAQTLSAILLAFIITWTPYNIMVLVSTFCDKCVPVTLWH
LGYWLCYVNSTVNPICYALCNRTFRKTFKMLLLCRWKKKKVEE

Ligands and cofactors

ID	Name	Formula	Copies
ACH	Acetylcholine	C7 H16 N O2	1
A1BKS	VU6007678	C25 H29 F N4 O3 S	1

Primary citation

Cryo-EM reveals an extrahelical allosteric binding site at the M 5 mAChR. Burger, W.A.C., Mobbs, J.I., Rana, B. et al. Nat Commun (2025) 16:7046-7046. DOI 10.1038/s41467-025-62212-z · PubMed

Other PDB entries of the same protein (UniProt P54311 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7MBX 1.95 Å, Human Cholecystokinin 1 receptor (CCK1R) Gs complex
9IJE 2.34 Å, Epinephrine-activated human beta3 adrenergic receptor
8YK0 2.4 Å, Cryo-EM structure of human GPR156-Gi3 complex
8Z9O 2.4 Å, Cryo-EM structure of human GPR4-Gs complex
22ES 2.43 Å, Gi bound kappa-opioid receptor in complex with difelikefalin
7MBY 2.44 Å, Human Cholecystokinin 1 receptor (CCK1R) Gq chimera (mGsqi) complex
9WG6 2.44 Å, D1R-Gs in complexed with Dopamine/LY3154207/BMSA1/UNC9815
8JIS 2.46 Å, Cryo-EM structure of the GLP-1R/GCGR dual agonist peptide15-bound human GLP-1R-Gs complex
9M0R 2.47 Å, Structure of neuropeptide FF receptor 1 complex with NPVF
8YKV 2.48 Å, Cryo-EM structure of succinate receptor SUCR1 bound to compound 31
9M1O 2.49 Å, Cryo-EM structures of NPFFR2 complex with neuropeptide FF
7DUQ 2.5 Å, Cryo-EM structure of the compound 2 and GLP-1-bound human GLP-1 receptor-Gs complex

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