9XN3: PDB entry 9XN3
Glucose-dependent insulinotropic polypeptide receptor-Gs complex activated by the small molecule agonist SIM1. Determined by electron microscopy at 2.74 Å resolution. Released 30 Sept 2026.
- Method
- Electron microscopy
- Resolution
- 2.74 Å
- Organisms
- Bos taurus, Rattus norvegicus, Lama glama
- Chains
- 5
- Atoms
- 8,542
- Mol. weight
- 148.66 kDa
- Ligands
- A1E0Y
- Released
- 30 Sept 2026
Explore 9XN3 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9XN3 contains 38 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: 15 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-32 | 26 | |
| β-strand | 33-40 | 8 | 1 |
| α-helix | 46-53 | 8 | |
| α-helix | 54-56 | 3 | |
| α-helix | 63-84 | 22 | |
| α-helix | 152-157 | 6 | |
| α-helix | 159-163 | 5 | |
| α-helix | 171-177 | 7 | |
| β-strand | 184-191 | 8 | 1 |
| β-strand | 194-201 | 8 | 1 |
| α-helix | 212-215 | 4 | |
| β-strand | 220-226 | 7 | 1 |
| α-helix | 233-244 | 12 | |
| α-helix | 248-250 | 3 | |
| β-strand | 253-259 | 7 | 1 |
| α-helix | 261-268 | 8 | |
| α-helix | 280-283 | 4 | |
| α-helix | 293-294 | 2 | |
| α-helix | 299-317 | 19 | |
| β-strand | 326-330 | 5 | 1 |
| α-helix | 338-357 | 20 | |
Chain B: 4 helices, 28 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-30 | 22 | |
| α-helix | 35-38 | 4 | |
| α-helix | 39-41 | 3 | |
| α-helix | 43-44 | 2 | |
| β-strand | 52-56 | 5 | 2 |
| β-strand | 63-68 | 6 | 3 |
| β-strand | 74-79 | 6 | 3 |
| β-strand | 83-88 | 6 | 3 |
| β-strand | 94-99 | 6 | 3 |
| β-strand | 105-110 | 6 | 4 |
| β-strand | 116-121 | 6 | 4 |
| β-strand | 125-130 | 6 | 4 |
| β-strand | 139-145 | 7 | 4 |
| β-strand | 151-158 | 8 | 5 |
| β-strand | 161-166 | 6 | 5 |
| β-strand | 170-175 | 6 | 5 |
| β-strand | 180-186 | 7 | 5 |
| β-strand | 192-197 | 6 | 6 |
| β-strand | 203-208 | 6 | 6 |
| β-strand | 212-217 | 6 | 6 |
| β-strand | 223-228 | 6 | 6 |
| β-strand | 234-239 | 6 | 7 |
| β-strand | 245-250 | 6 | 7 |
| β-strand | 255-259 | 5 | 7 |
| β-strand | 264-269 | 6 | 7 |
| β-strand | 278-283 | 6 | 8 |
| β-strand | 289-294 | 6 | 8 |
| β-strand | 299-303 | 5 | 8 |
| β-strand | 308-313 | 6 | 8 |
| β-strand | 320-325 | 6 | 2 |
| β-strand | 332-336 | 5 | 2 |
| β-strand | 341-344 | 4 | 2 |
Chain C: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-23 | 16 | |
| α-helix | 30-43 | 14 | |
| α-helix | 53-55 | 3 | |
Chain N: 3 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5-9 | 5 | 9 |
| β-strand | 12-13 | 2 | 10 |
| β-strand | 19-27 | 9 | 9 |
| α-helix | 31-33 | 3 | |
| β-strand | 36-41 | 6 | 10 |
| β-strand | 47-53 | 7 | 10 |
| β-strand | 60-62 | 3 | 10 |
| α-helix | 64-66 | 3 | |
| β-strand | 70-75 | 6 | 9 |
| β-strand | 80-86 | 7 | 9 |
| α-helix | 90-92 | 3 | |
| β-strand | 94-100 | 7 | 10 |
| β-strand | 120 | 1 | 10 |
| β-strand | 124-127 | 4 | 10 |
Chain R: 13 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 131-161 | 31 | |
| α-helix | 163-165 | 3 | |
| α-helix | 168-193 | 26 | |
| α-helix | 213-246 | 34 | |
| α-helix | 253-255 | 3 | |
| α-helix | 256-281 | 26 | |
| α-helix | 293-328 | 36 | |
| α-helix | 332-346 | 15 | |
| α-helix | 349-355 | 7 | |
| α-helix | 370-382 | 13 | |
| α-helix | 384-389 | 6 | |
| α-helix | 390-394 | 5 | |
| α-helix | 397-409 | 13 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Guanine nucleotide-binding protein G(s) subunit alpha | A | protein | 361 | Bos taurus | |
| Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | B | protein | 345 | Rattus norvegicus | P54311 (AlphaFold model) |
| Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | C | protein | 71 | Bos taurus | P63212 (AlphaFold model) |
| Nanobody-35 | N | protein | 130 | Lama glama | |
| Gastric inhibitory polypeptide receptor | R | protein | 400 | Homo sapiens | P48546 (AlphaFold model) |
Sequence of entity 1 (A), FASTA
>9XN3_1 Guanine nucleotide-binding protein G(s) subunit alpha (chains A)
MGCTLSAEDKAAVERSKMIEKQLQKDKQVYRATHRLLLLGADNSGKSTIVKQMRIYHVNG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TSGIFETKFQVDKVNFHMFDVGAQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQEALNDF
KSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEPGEDPR
VTRAKYFIRDEFLRISTASGDGRHYCYPHFTCSVDTENARRIFNDCRDIIQRMHLRQYEL
L
Sequence of entity 2 (B), FASTA
>9XN3_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHL
AKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACG
GLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQ
QTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFF
PNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCN
VWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN
Sequence of entity 3 (C), FASTA
>9XN3_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL
Sequence of entity 4 (N), FASTA
>9XN3_4 Nanobody-35 (chains N)
MAQVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVRQAPGKGLEWVSDISQSGASI
SYTGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCARCPAPFTRDCFDVTSTTYAYR
GQGTQVTVSS
Sequence of entity 5 (R), FASTA
>9XN3_5 Gastric inhibitory polypeptide receptor (chains R)
RAETGSKGQTAGELYQRWERYRRECQETLAAAEPPSGLACNGSFDMYVCWDYAAPNATAR
ASCPWYLPWHHHVAAGFVLRQCGSDGQWGLWRDHTQCENPEKNEAFLDQRLILERLQVMY
TVGYSLSLATLLLALLILSLFRRLHCTRNYIHINLFTSFMLRAAAILSRDRLLPRPGPYL
GDQALALWNQALAACRTAQIVTQYCVGANYTWLLVEGVYLHSLLVLVGGSEEGHFRYYLL
LGWGAPALFVIPWVIVRYLYENTQCWERNEVKAIWWIIRTPILMTILINFLIFIRILGIL
LSKLRTRQMRCRDYRLRLARSTLTLVPLLGVHEVVFAPVTEEQARGALRFAKLGFEIFLS
SFQGFLVSVLYCFINKEVQSEIRRGWHHCRLRRSLGEEQR
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| A1E0Y | 1-[3,5-dimethyl-4-[2-[[4-oxidanylidene-2-[4-(trifluoromethyloxy)phenyl]-1,3,8-t… | C28 H29 F3 N4 O6 S | 1 |
Primary citation
Structural basis for small-molecule agonism at GCGR and GIPR via a conserved intracellular allosteric site. He, Q., Shan, H., Hu, W. et al. Acta Pharmacol Sin (2026). DOI 10.1038/s41401-026-01923-5 · 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
- 9EJZ 2.06 Å, Human M5 muscarinic acetylcholine receptor complex with mini-Gq, agonist acetylcholine…
- 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
Browse structure collections
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