8F2B: Amylin 3 Receptor

Amylin 3 Receptor in complex with Gs and Pramlintide analogue peptide San45. Determined by electron microscopy at 2.0 Å resolution. Released 2 Aug 2023.

Method: Electron microscopy
Resolution: 2.0 Å
Organisms: Homo sapiens, Lama glama
Chains: 7
Atoms: 10,360
Mol. weight: 191.39 kDa
Ligands: NAG, D6M, Y01, P42
Released: 2 Aug 2023

Explore 8F2B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8F2B contains 53 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	12-39	28
β-strand	41-46	6	1
α-helix	53-58	6
β-strand	207-214	8	1
β-strand	217-224	8	1
α-helix	234-238	5
β-strand	243-249	7	1
α-helix	265-278	14
β-strand	286-292	7	1
α-helix	294-303	10
α-helix	308-310	3
α-helix	313-315	3
α-helix	332-351	20
β-strand	359-363	5	1
α-helix	371-390	20

Chain B: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-25	22
α-helix	30-33	4
α-helix	38-39	2
β-strand	47-51	5	2
β-strand	58-63	6	3
β-strand	69-74	6	3
β-strand	78-83	6	3
β-strand	88-94	7	3
β-strand	100-105	6	4
β-strand	111-116	6	4
β-strand	121-125	5	4
β-strand	134-139	6	4
β-strand	146-153	8	5
β-strand	156-161	6	5
β-strand	166-170	5	5
β-strand	175-180	6	5
β-strand	187-192	6	6
β-strand	198-203	6	6
β-strand	208-212	5	6
β-strand	218-222	5	6
β-strand	229-234	6	7
β-strand	240-245	6	7
β-strand	250-254	5	7
β-strand	259-264	6	7
β-strand	273-278	6	8
β-strand	284-289	6	8
β-strand	294-298	5	8
β-strand	304-308	5	8
β-strand	315-320	6	2
β-strand	327-331	5	2
β-strand	336-339	4	2

Chain E: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	31-50	20
α-helix	59-61	3
α-helix	63-79	17
α-helix	82-83	2
α-helix	89-99	11
α-helix	113-115	3
α-helix	116-140	25

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-23	15
α-helix	30-43	14
α-helix	54-55	2

Chain N: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	10-12	3	10
β-strand	18-25	8	9
α-helix	29-31	3
β-strand	34-39	6	10
β-strand	45-51	7	10
β-strand	58-60	3	10
α-helix	62-64	3
β-strand	68-73	6	9
β-strand	78-83	6	9
α-helix	88-90	3
β-strand	92-98	7	10
β-strand	118	1	10
β-strand	122-126	5	10

Chain P: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	4	1	11
α-helix	5-7	3
α-helix	8-18	11
α-helix	25-26	2
α-helix	29-31	3

Chain R: 24 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	42-61	20
α-helix	63-65	3
β-strand	71-72	2	12
α-helix	73-74	2
β-strand	75-76	2	13
β-strand	81-82	2	13
β-strand	85-86	2	12
β-strand	90-94	5	14
α-helix	95-96	2
β-strand	107-111	5	14
β-strand	112	1	15
β-strand	118	1	15
β-strand	120-121	2	16
β-strand	126-127	2	16
β-strand	130	1	14
α-helix	132-135	4
α-helix	138-172	35
α-helix	174-176	3
α-helix	179-200	22
α-helix	201-205	5
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	271-281	11
α-helix	288-290	3
α-helix	296-298	3
α-helix	299-329	31
α-helix	334-352	19
α-helix	355-358	4
β-strand	361	1	11
α-helix	366-381	16
α-helix	383-388	6
α-helix	389-393	5
α-helix	396-408	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
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 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	71	Homo sapiens	P59768 (AlphaFold model)
nanobody 35	N	protein	138	Lama glama
Receptor activity-modifying protein 3	E	protein	149	Homo sapiens	O60896 (AlphaFold model)
pramlintide analogue San45	P	protein	38	Homo sapiens	P10997
Calcitonin receptor	R	protein	501	Homo sapiens	P30988

Sequence of entity 1 (A), FASTA

>8F2B_1 Guanine nucleotide-binding protein G(s) subunit alpha isoforms short (chains A)
MGCLGNSKTEDQRNEEKAQREANKKIEKQLQKDKQVYRATHRLLLLGAGESGKNTIVKQM
RILHVNGFNGEGGEEDPQAARSNSDGEKATKVQDIKNNLKEAIETIVAAMSNLVPPVELA
NPENQFRVDYILSVMNVPDFDFPPEFYEHAKALWEDEGVRACYERSNEYQLIDCAQYFLD
KIDVIKQADYVPSDQDLLRCRVLTSGIFETKFQVDKVNFHMFDVGAQRDERRKWIQCFND
VTAIIFVVASSSYNMVIREDNQTNRLQAALKLFDSIWNNKWLRDTSVILFLNKQDLLAEK
VLAGKSKIEDYFPEFARYTTPEDATPEPGEDPRVTRAKYFIRDEFLRISTASGDGRHYCY
PHFTCAVDTENIRRVFNDCRDIIQRMHLRQYELL

Sequence of entity 2 (B), FASTA

>8F2B_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

>8F2B_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (N), FASTA

>8F2B_4 nanobody 35 (chains N)
QVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVRQAPGKGLEWVSDISQSGASISY
TGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCARCPAPFTRDCFDVTSTTYAYRGQ
GTQVTVSSHHHHHHEPEA

Sequence of entity 5 (E), FASTA

>8F2B_5 Receptor activity-modifying protein 3 (chains E)
MKTIIALSYIFCLVFADYKDDDDKRAGGCNETGMLERLPLCGKAFADMMGKVDVWKWCNL
SEFIVYYESFTNCTEMEANVVGCYWPNPLAQGFITGIHRQFFSNCTVDRVHLEDPPDEVL
IPLIVIPVVLTVAMAGLVVWRSKRTDTLL

Sequence of entity 6 (P), FASTA

>8F2B_6 pramlintide analogue San45 (chains P)
KCNTATCATQRLANFLVHSSKNFGPILPPTNVGSNTYX

Sequence of entity 7 (R), FASTA

>8F2B_7 Calcitonin receptor (chains R)
MKTIIALSYIFCLVFADYKDDDDLEVLFQGPAAFSNQTYPTIEPKPFLYVVGRKKMMDAQ
YKCYDRMQQLPAYQGEGPYCNRTWDGWLCWDDTPAGVLSYQFCPDYFPDFDPSEKVTKYC
DEKGVWFKHPENNRTWSNYTMCNAFTPEKLKNAYVLYYLAIVGHSLSIFTLVISLGIFVF
FRSLGCQRVTLHKNMFLTYILNSMIIIIHLVEVVPNGELVRRDPVSCKILHFFHQYMMAC
NYFWMLCEGIYLHTLIVVAVFTEKQRLRWYYLLGWGFPLVPTTIHAITRAVYFNDNCWLS
VETHLLYIIHGPVMAALVVNFFFLLNIVRVLVTKMRETHEAESHMYLKAVKATMILVPLL
GIQFVVFPWRPSNKMLGKIYDYVMHSLIHFQGFFVATIYCFCNNEVQTTVKRQWAQFKIQ
WNQRWGRRPSNRSARAAAAAAEAGDIPIYICHQELRNEPANNQGEESAEIIPLNIIEQES
SAPAGLEVLFQGPHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3
D6M	N-hexadecanoyl-L-glutamic acid	C21 H39 N O5	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
PLM	Palmitic acid	C16 H32 O2	8

Primary citation

Structural insight into selectivity of amylin and calcitonin receptor agonists. Cao, J., Belousoff, M.J., Gerrard, E. et al. Nat Chem Biol (2024) 20:162-169. DOI 10.1038/s41589-023-01393-4 · PubMed

Other PDB entries of the same protein (UniProt P63092 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7BPH 1.57 Å, Crystal structure of GppNHp-bound GNAS in complex with the cyclic peptide inhibitor GN13
6AU6 1.7 Å, Crystal structure of GDP-bound human GNAS R201C mutant
8F0K 1.9 Å, Human Amylin3 Receptor in complex with Gs and Pramlintide analogue peptide San385
7E5E 1.95 Å, Crystal structure of GDP-bound GNAS in complex with the cyclic peptide inhibitor GD20
7MBX 1.95 Å, Human Cholecystokinin 1 receptor (CCK1R) Gs complex
8F0J 2.0 Å, Calcitonin Receptor in complex with Gs and Pramlintide analogue peptide San45
9XXT 2.0 Å, Cryo-EM structure of lysophosphatidylserine (18:0)-bound GPR174-Gs complex
6X18 2.1 Å, GLP-1 peptide hormone bound to Glucagon-Like peptide-1 (GLP-1) Receptor
6X19 2.1 Å, Non peptide agonist CHU-128, bound to Glucagon-Like peptide-1 (GLP-1) Receptor
9NTU 2.1 Å, Cryo-EM structure of BETP-GLP-1(9-36)-GLP-1R-Gs complex
7RTB 2.14 Å, Peptide-19 bound to the Glucagon-Like Peptide-1 Receptor (GLP-1R)
7TYF 2.2 Å, Human Amylin1 Receptor in complex with Gs and rat amylin peptide

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