8JR9: Small molecule agonist
Small molecule agonist (PCO371) bound to human parathyroid hormone receptor type 1 (PTH1R). Determined by electron microscopy at 2.57 Å resolution. Released 2 Aug 2023.
- Method
- Electron microscopy
- Resolution
- 2.57 Å
- Organisms
- Bos taurus, Rattus norvegicus, Lama glama
- Chains
- 5
- Atoms
- 7,893
- Mol. weight
- 158.83 kDa
- Ligands
- KHF
- Released
- 2 Aug 2023
Explore 8JR9 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8JR9 contains 31 α-helices and 45 β-strands across 5 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 | 6-32 | 27 | |
| β-strand | 34-40 | 7 | 1 |
| α-helix | 46-52 | 7 | |
| α-helix | 53-56 | 4 | |
| 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 | 266-277 | 12 | |
| β-strand | 286-292 | 7 | 1 |
| α-helix | 294-303 | 10 | |
| α-helix | 313-315 | 3 | |
| α-helix | 332-352 | 21 | |
| β-strand | 359-363 | 5 | 1 |
| α-helix | 371-390 | 20 | |
Chain B: 4 helices, 28 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-24 | 21 | |
| α-helix | 30-34 | 5 | |
| β-strand | 46-52 | 7 | 2 |
| β-strand | 58-63 | 6 | 3 |
| β-strand | 69-74 | 6 | 3 |
| β-strand | 78-83 | 6 | 3 |
| β-strand | 89-94 | 6 | 3 |
| α-helix | 95 | 1 | |
| β-strand | 100-105 | 6 | 4 |
| β-strand | 111-116 | 6 | 4 |
| β-strand | 121-125 | 5 | 4 |
| β-strand | 135-139 | 5 | 4 |
| α-helix | 145 | 1 | |
| β-strand | 146-151 | 6 | 5 |
| β-strand | 156-161 | 6 | 5 |
| β-strand | 166-170 | 5 | 5 |
| β-strand | 176-180 | 5 | 5 |
| β-strand | 187-192 | 6 | 6 |
| β-strand | 198-203 | 6 | 6 |
| β-strand | 207-212 | 6 | 6 |
| β-strand | 218-223 | 6 | 6 |
| β-strand | 229-234 | 6 | 7 |
| β-strand | 240-245 | 6 | 7 |
| β-strand | 249-254 | 6 | 7 |
| β-strand | 260-265 | 6 | 7 |
| β-strand | 276-278 | 3 | 8 |
| β-strand | 284-287 | 4 | 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 | 335-340 | 6 | 2 |
Chain G: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-21 | 14 | |
| α-helix | 30-43 | 14 | |
| α-helix | 53-55 | 3 | |
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 | 17-25 | 9 | 9 |
| 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 | 78-84 | 7 | 9 |
| α-helix | 88-90 | 3 | |
| β-strand | 92-98 | 7 | 10 |
| α-helix | 109-111 | 3 | |
| β-strand | 118 | 1 | 10 |
| β-strand | 122-126 | 5 | 10 |
Chain R: 12 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 186-211 | 26 | |
| α-helix | 213-215 | 3 | |
| α-helix | 218-242 | 25 | |
| α-helix | 279-311 | 33 | |
| α-helix | 317-346 | 30 | |
| α-helix | 357-360 | 4 | |
| α-helix | 361-392 | 32 | |
| α-helix | 400-413 | 14 | |
| α-helix | 416-426 | 11 | |
| α-helix | 437-456 | 20 | |
| α-helix | 457-461 | 5 | |
| α-helix | 464-480 | 17 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Guanine nucleotide-binding protein G(s) subunit alpha-1 | A | protein | 361 | Bos taurus | P63092 (AlphaFold model), P63096 (AlphaFold model) |
| Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | B | protein | 352 | Rattus norvegicus | P62873 (AlphaFold model) |
| Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | G | protein | 71 | Bos taurus | P59768 (AlphaFold model) |
| Nanobody 35 | N | protein | 140 | Lama glama | |
| Parathyroid hormone/parathyroid hormone-related peptide receptor | R | protein | 478 | Homo sapiens | Q03431 |
Sequence of entity 1 (A), FASTA
>8JR9_1 Guanine nucleotide-binding protein G(s) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIEKQLQKDKQVYRATHRLLLLGADNSGKSTIVKQMRIYHVNG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TSGIFETKFQVDKVNFHMFDVGAQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQEALNDF
KSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEPGEDPR
VTRAKYFIRDEFLRISTASGDGRHYCYPHFTCSVDTENARRIFNDCRDIIQRMHLRQYEL
L
Sequence of entity 2 (B), FASTA
>8JR9_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
GSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLA
KIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGG
LDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQ
TTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFP
NGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNV
WDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWNGSSGGGGS
Sequence of entity 3 (G), FASTA
>8JR9_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL
Sequence of entity 4 (N), FASTA
>8JR9_4 Nanobody 35 (chains N)
MAQVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVRQAPGKGLEWVSDISQSGASI
SYTGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCARCPAPFTRDCFDVTSTTYAYR
GQGTQVTVSSHHHHHHEPEA
Sequence of entity 5 (R), FASTA
>8JR9_5 Parathyroid hormone/parathyroid hormone-related peptide receptor (chains R)
DADDVMTKEEQIFLLHRAQAQCEKRLKEVLQRPASIMESDKGWTSASTSGKPRKDKASGK
LYPESEEDKEAPTGSRYRGRPCLPEWDHILCWPLGAPGEVVAVPCPDYIYDFNHKGHAYR
RCDRNGSWELVPGHNRTWANYSECVKFLTNETREREVFDRLAMIYTVGYSVSLASLTVAV
LILAYFRRLHCTRNYIHMHLFLSFMLRAVSIFVKDAVLYSGATLDEAERLTEEELRAIAQ
APPPPATAAAGYAGCRVAVTFFLYFLATNYYWILVEGLYLHSLIFMAFFSEKKYLWGFTV
FGWGLPAVFVAVWVSVRATLANTGCWDLSSGNKKWIIQVPILASIVLNFILFINIVRVLA
TKLRETNAGRCDTRQQYRKLLKSTLVLMPLFGVHYIVFMATPYTEVSGTLWQVQMHYEML
FNSFQGFFVAIIYCFCNGEVQAEIKKSWSRWTLALDFRRKARSGSSSYSYGPMVSHEF
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| KHF | PCO-371 | C29 H32 F3 N5 O6 S | 1 |
Primary citation
Conserved class B GPCR activation by a biased intracellular agonist. Zhao, L.H., He, Q., Yuan, Q. et al. Nature (2023) 621:635-641. DOI 10.1038/s41586-023-06467-w · 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
- 8F2B 2.0 Å, Amylin 3 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)
Browse structure collections
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