9BP3: Human Amylin1 Receptor

Human Amylin1 Receptor in complex with Gs and cagrilintide. Determined by electron microscopy at 2.2 Å resolution. Released 23 Apr 2025.

Method: Electron microscopy
Resolution: 2.2 Å
Organisms: Homo sapiens, Lama glama
Chains: 7
Atoms: 10,131
Mol. weight: 184.93 kDa
Ligands: NAG, A1B90, Y01, P42
Released: 23 Apr 2025

Explore 9BP3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9BP3 contains 50 α-helices and 58 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: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	12-38	27
β-strand	40-46	7	7
α-helix	53-59	7
β-strand	207-214	8	7
β-strand	217-224	8	7
α-helix	234-238	5
β-strand	243-249	7	7
α-helix	265-278	14
α-helix	280-282	3
β-strand	286-292	7	7
α-helix	294-302	9
α-helix	313-317	5
α-helix	332-352	21
β-strand	359-363	5	7
α-helix	370-390	21

Chain B: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	3-24	22
α-helix	30-33	4
α-helix	38-39	2
β-strand	47-51	5	8
β-strand	58-63	6	9
β-strand	69-74	6	9
β-strand	78-83	6	9
β-strand	89-94	6	9
β-strand	100-105	6	10
β-strand	111-116	6	10
β-strand	121-125	5	10
β-strand	134-139	6	10
β-strand	146-151	6	11
β-strand	156-161	6	11
β-strand	166-170	5	11
β-strand	175-180	6	11
β-strand	187-192	6	12
β-strand	198-203	6	12
β-strand	207-212	6	12
β-strand	218-223	6	12
β-strand	229-234	6	13
β-strand	240-245	6	13
β-strand	250-254	5	13
β-strand	259-264	6	13
β-strand	273-278	6	14
β-strand	284-289	6	14
β-strand	294-298	5	14
β-strand	304-308	5	14
β-strand	315-320	6	8
β-strand	327-331	5	8
β-strand	336-339	4	8

Chain E: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	35-51	17
α-helix	62-79	18
α-helix	87-100	14
α-helix	104-106	3
α-helix	113-115	3
α-helix	116-143	28

Chain G: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	9-22	14
α-helix	30-43	14
α-helix	53-55	3
α-helix	56-58	3

Chain N: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	15
β-strand	10-12	3	16
β-strand	17-25	9	15
α-helix	29-31	3
β-strand	34-39	6	16
β-strand	45-51	7	16
β-strand	58-60	3	16
α-helix	62-64	3
β-strand	68-73	6	15
β-strand	78-84	7	15
α-helix	88-90	3
β-strand	92-98	7	16
β-strand	118	1	16
β-strand	122-126	5	16

Chain P: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	4	1	1
α-helix	5-7	3
α-helix	8-19	12
α-helix	21-23	3
α-helix	25-31	7

Chain R: 21 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	42-61	20
β-strand	71-72	2	2
α-helix	73-74	2
β-strand	75-76	2	3
β-strand	81-82	2	3
β-strand	85-86	2	2
β-strand	90-94	5	4
α-helix	95-96	2
β-strand	107-111	5	4
β-strand	112	1	5
β-strand	118	1	5
β-strand	120-121	2	6
β-strand	126-127	2	6
β-strand	130	1	4
α-helix	132-136	5
α-helix	138-172	35
α-helix	174-176	3
α-helix	179-204	26
α-helix	209-214	6
α-helix	217-245	29
α-helix	246-250	5
α-helix	260-263	4
α-helix	264-268	5
α-helix	271-283	13
α-helix	288-290	3
α-helix	296-298	3
α-helix	299-329	31
α-helix	334-352	19
α-helix	354-358	5
β-strand	361	1	1
α-helix	366-388	23
α-helix	389-393	5
α-helix	396-408	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Receptor activity-modifying protein 1	E	protein	149	Homo sapiens	O60894 (AlphaFold model)
Cagrilintide	P	protein	39	Homo sapiens	P10997 (AlphaFold model)
Calcitonin receptor	R	protein	462	Homo sapiens	P30988 (AlphaFold model)
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short	A	protein	394	Homo sapiens	P63092 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	350	Homo sapiens	P62873
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	71	Homo sapiens	P59768
Nanobody 35	N	protein	138	Lama glama

Sequence of entity 1 (E), FASTA

>9BP3_1 Receptor activity-modifying protein 1 (chains E)
MKTIIALSYIFCLVFADYKDDDDKHGSCQEANYGALLRELCLTQFQVDMEAVGETLWCDW
GRTIRSYRELADCTWHMAEKLGCFWPNAEVDRFFLAVHGRYFRSCPISGRAVRDPPGSIL
YPFIVVPITVTLLVTALVVWQSKRTEGIV

Sequence of entity 2 (P), FASTA

>9BP3_2 Cagrilintide (chains P)
EKCNTATCATQRLAEFLRHSSNNFGPILPPTNVGSNTPX

Sequence of entity 3 (R), FASTA

>9BP3_3 Calcitonin receptor (chains R)
GPAAFSNQTYPTIEPKPFLYVVGRKKMMDAQYKCYDRMQQLPAYQGEGPYCNRTWDGWLC
WDDTPAGVLSYQFCPDYFPDFDPSEKVTKYCDEKGVWFKHPENNRTWSNYTMCNAFTPEK
LKNAYVLYYLAIVGHSLSIFTLVISLGIFVFFRSLGCQRVTLHKNMFLTYILNSMIIIIH
LVEVVPNGELVRRDPVSCKILHFFHQYMMACNYFWMLCEGIYLHTLIVVAVFTEKQRLRW
YYLLGWGFPLVPTTIHAITRAVYFNDNCWLSVETHLLYIIHGPVMAALVVNFFFLLNIVR
VLVTKMRETHEAESHMYLKAVKATMILVPLLGIQFVVFPWRPSNKMLGKIYDYVMHSLIH
FQGFFVATIYCFCNNEVQTTVKRQWAQFKIQWNQRWGRRPSNRSARAAAAAAEAGDIPIY
ICHQELRNEPANNQGEESAEIIPLNIIEQESSAPAGLEVLFQ

Sequence of entity 4 (A), FASTA

>9BP3_4 Guanine nucleotide-binding protein G(s) subunit alpha isoforms short (chains A)
MGCLGNSKTEDQRNEEKAQREANKKIEKQLQKDKQVYRATHRLLLLGAGESGKNTIVKQM
RILHVNGFNGEGGEEDPQAARSNSDGEKATKVQDIKNNLKEAIETIVAAMSNLVPPVELA
NPENQFRVDYILSVMNVPDFDFPPEFYEHAKALWEDEGVRACYERSNEYQLIDCAQYFLD
KIDVIKQADYVPSDQDLLRCRVLTSGIFETKFQVDKVNFHMFDVGAQRDERRKWIQCFND
VTAIIFVVASSSYNMVIREDNQTNRLQAALKLFDSIWNNKWLRDTSVILFLNKQDLLAEK
VLAGKSKIEDYFPEFARYTTPEDATPEPGEDPRVTRAKYFIRDEFLRISTASGDGRHYCY
PHFTCSVDTENIRRVFNDCRDIIQRMHLRQYELL

Sequence of entity 5 (B), FASTA

>9BP3_5 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRT
LRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGN
YVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWD
IETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDIN
AICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYD
DFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 6 (G), FASTA

>9BP3_6 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 7 (N), FASTA

>9BP3_7 Nanobody 35 (chains N)
QVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVRQAPGKGLEWVSDISQSGASISY
TGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCARCPAPFTRDCFDVTSTTYAYRGQ
GTQVTVSSHHHHHHEPEA

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3
A1B90	icosanedioic acid	C20 H38 O4	1
Y01	Cholesterol hemisuccinate	C31 H50 O4	2
P42	(2S)-2-{[(1R)-1-hydroxyhexadecyl]oxy}-3-{[(1R)-1-hydroxyoctadecyl]oxy}propyl…	C42 H88 N O8 P	1

Primary citation

Structural and dynamic features of cagrilintide binding to calcitonin and amylin receptors. Cao, J., Belousoff, M.J., Johnson, R.M. et al. Nat Commun (2025) 16:3389-3389. DOI 10.1038/s41467-025-58680-y · PubMed

Other PDB entries of the same protein (UniProt O60894 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6ZHO 1.6 Å, Crystal structure of a CGRP receptor ectodomain heterodimer with bound high affinity…
8AX7 1.65 Å, Crystal structure of a CGRP receptor ectodomain heterodimer bound to macrocyclic…
7P0F 1.85 Å, Crystal structure of a CGRP receptor ectodomain heterodimer bound to macrocyclic…
8AX6 1.9 Å, Crystal structure of a CGRP receptor ectodomain heterodimer bound to macrocyclic…
6D1U 2.05 Å, Crystal structure of the human CLR:RAMP1 extracellular domain heterodimer in complex…
3N7S 2.1 Å, Crystal structure of the ectodomain complex of the CGRP receptor, a Class-B GPCR,…
7TYF 2.2 Å, Human Amylin1 Receptor in complex with Gs and rat amylin peptide
7P0I 2.3 Å, Crystal structure of a CGRP receptor ectodomain heterodimer bound to macrocyclic…
2YX8 2.4 Å, Crystal structure of the extracellular domain of human RAMP1
9AUC 2.4 Å, Human Amylin1 Receptor in Complex with Gs and human Calcitonin Gene-Related Peptide
4RWG 2.44 Å, Crystal structure of the CLR:RAMP1 extracellular domain heterodimer with bound high…
6UMG 2.7 Å, Crystal structure of erenumab Fab bound to the extracellular domain of CGRP receptor

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