9UCP: PDB entry 9UCP

cryo-EM structure of M1 muscarinic acetylcholine receptor-alpha5 helix of G11 protein complex bound to iperoxo and nanobody Nb1B4. Determined by electron microscopy at 2.88 Å resolution. Released 29 Oct 2025.

Method: Electron microscopy
Resolution: 2.88 Å
Organisms: Homo sapiens, Vicugna pacos
Chains: 3
Atoms: 3,529
Mol. weight: 66.43 kDa
Ligands: IXO
Released: 29 Oct 2025

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

Secondary structure: helices and β-sheets

9UCP contains 25 α-helices and 15 β-strands across 3 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: 22 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	25-52	28
α-helix	59-61	3
α-helix	62-73	12
α-helix	74-78	5
α-helix	79-87	9
α-helix	94-128	35
α-helix	130-136	7
α-helix	139-167	29
α-helix	174	1
β-strand	175	1	1
β-strand	177	1	1
α-helix	188-193	6
α-helix	194-198	5
α-helix	199-231	33
α-helix	234-246	13
α-helix	250-261	12
α-helix	267-271	5
α-helix	275-287	13
α-helix	293-308	16
α-helix	315-350	36
α-helix	357-366	10
α-helix	369-373	5
α-helix	374-376	3
α-helix	388-391	4

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	334-355	22

Chain C: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	2
β-strand	10	1	3
β-strand	23-24	2	2
β-strand	33-39	7	4
β-strand	47-52	6	4
β-strand	58-59	2	4
β-strand	69-72	4	5
β-strand	77-80	4	5
α-helix	87-89	3
β-strand	91	1	6
β-strand	92-95	4	4
α-helix	103-105	3
β-strand	115	1	4
β-strand	117	1	3
β-strand	118	1	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
M1 muscarinic acetylcholine receptor, de novo design protein	A	protein	435	Homo sapiens
Guanine nucleotide-binding protein subunit alpha-11	B	protein	27	Homo sapiens	P29992 (AlphaFold model)
Nanobody Nb1B4	C	protein	122	Vicugna pacos

Sequence of entity 1 (A), FASTA

>9UCP_1 M1 muscarinic acetylcholine receptor, de novo design protein (chains A)
DYKDDDDAAAQTSAPPAVSPQITVLAPGKGPWQVAFIGITTGLLSLATVTGNLLVLISFK
VNTELKTVNNYFLLSLACADLIIGTFSMNLYTTYLLMGHWALGTLACDLWLALDYVASNA
SVMNLLLISFDRYFSVTRPLSYRAKRTPRRAALMIGLAWLVSFVLWAPAILFWQYLVGER
TVLAGQCYIQFLSQPIITFGTAMAAFYLPVTVMCTLYWRIYRETKRAGERLAKLLEKFEA
LPLEDIVAALKALLATNRPEIQLAVKTIVENFPEIKKEAEKLTPEQKAKLAALEAQLADL
PEELRKVLLSMYLTGLLYGGSEENRKRAIEKAARTLSAILLAFILTWTPYNIMVLVSTFC
KDCVPETLWELGYWLCYVNSTINPMCYALCNKAFRDTFRLLLLCRWDKRRWRKIPKRPGS
VHRTPSRQCHHHHHH

Sequence of entity 2 (B), FASTA

>9UCP_2 Guanine nucleotide-binding protein subunit alpha-11 (chains B)
TPENIRFVFAAVKDTILQLNLKEYNLV

Sequence of entity 3 (C), FASTA

>9UCP_3 Nanobody Nb1B4 (chains C)
QVQLQESGGGLVQAGGSLRLSCAASGSIFYGYYMGWYRQAPGKEREFVATINYGASTNYA
DSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAVRRVYVYVQRYYHYYWGQGTQVTV
SS

Ligands and cofactors

ID	Name	Formula	Copies
IXO	4-(4,5-dihydro-1,2-oxazol-3-yloxy)-N,N,N-trimethylbut-2-yn-1-aminium	C10 H17 N2 O2	1

Primary citation

Extracellular nanobody screening using conformationally stable GPCR variants. Zhang, X., Gao, K., Nie, J. et al. Proc Natl Acad Sci U S A (2025) 122:e2508879122-e2508879122. DOI 10.1073/pnas.2508879122 · PubMed

Other PDB entries of the same protein (UniProt P29992 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8QEH 1.43 Å, Crystal structure of the G11 protein heterotrimer bound to FR900359 inhibitor
8QEG 1.7 Å, Crystal structure of the G11 protein heterotrimer bound to YM-254890 inhibitor
9P87 2.8 Å, NTSR1-G11-NTS(8-13) Complex in the Canonical, AHD Partially Closed State (C-P-Closed-Apo)
7XXH 2.9 Å, Cryo-EM structure of the purinergic receptor P2Y1R in complex with 2MeSADP and G11
9P86 2.9 Å, NTSR1-G11-NTS(8-13) Complex in the Canonical, AHD Open State (C-Open-Apo)
9P88 2.9 Å, NTSR1-G11-NTS(8-13) Complex in the Non-Canonical, AHD Open State (NC-Open-Apo)
6OIJ 3.3 Å, Muscarinic acetylcholine receptor 1-G11 protein complex
9UAP 3.62 Å, cryo-EM structure of ligand-free active-state M1 muscarinic acetylcholine receptor with…
7TRY 3.7 Å, Cryo-EM structure of corticotropin releasing factor receptor 2 bound to Urocortin 1 and…
9P8A 3.7 Å, NTSR1-G11-NTS(8-13) GTP-Bound Complex in the Canonical, AHD Closed State 3DVA Separated…
9P89 3.9 Å, NTSR1-G11-NTS(8-13) GTP-Bound Complex in the Canonical, AHD Closed State 3DVA Separated…
7RKF 4.0 Å, Structure of CX3CL1-US28-G11iN18-scFv16 in TL-state

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