9M0J: Bombesin receptor type-3
Cryo-EM structure of Bombesin receptor type-3 bound to oridonin. Determined by electron microscopy at 2.9 Å resolution. Released 4 Mar 2026.
- Method
- Electron microscopy
- Resolution
- 2.9 Å
- Organisms
- Homo sapiens, synthetic construct
- Chains
- 5
- Atoms
- 8,114
- Mol. weight
- 146.07 kDa
- Ligands
- ODN
- Released
- 4 Mar 2026
Explore 9M0J in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9M0J contains 29 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: 10 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-32 | 26 | |
| β-strand | 34-40 | 7 | 1 |
| α-helix | 46-52 | 7 | |
| β-strand | 185-190 | 6 | 1 |
| β-strand | 195-200 | 6 | 1 |
| β-strand | 220-226 | 7 | 1 |
| α-helix | 230-244 | 15 | |
| β-strand | 254-259 | 6 | 1 |
| α-helix | 261-270 | 10 | |
| α-helix | 275-277 | 3 | |
| α-helix | 280-284 | 5 | |
| α-helix | 286-288 | 3 | |
| α-helix | 293-294 | 2 | |
| α-helix | 299-317 | 19 | |
| β-strand | 326-330 | 5 | 1 |
| α-helix | 339-357 | 19 | |
Chain B: 3 helices, 28 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-29 | 21 | |
| α-helix | 35-39 | 5 | |
| 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 | 151-156 | 6 | 5 |
| β-strand | 161-166 | 6 | 5 |
| β-strand | 171-175 | 5 | 5 |
| β-strand | 180-185 | 6 | 5 |
| β-strand | 192-197 | 6 | 6 |
| β-strand | 203-208 | 6 | 6 |
| β-strand | 213-217 | 5 | 6 |
| β-strand | 223-227 | 5 | 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 | 298-303 | 6 | 8 |
| β-strand | 309-313 | 5 | 8 |
| β-strand | 320-325 | 6 | 2 |
| β-strand | 332-336 | 5 | 2 |
| β-strand | 341-344 | 4 | 2 |
Chain G: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-22 | 17 | |
| α-helix | 29-43 | 15 | |
| α-helix | 44-46 | 3 | |
Chain N: 1 helix, 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 |
| β-strand | 34-39 | 6 | 10 |
| β-strand | 45-51 | 7 | 10 |
| β-strand | 58-60 | 3 | 10 |
| 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 R: 12 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 51-74 | 24 | |
| α-helix | 83-107 | 25 | |
| α-helix | 117-149 | 33 | |
| α-helix | 161-179 | 19 | |
| α-helix | 180-183 | 4 | |
| α-helix | 212-222 | 11 | |
| α-helix | 223-227 | 5 | |
| α-helix | 228-250 | 23 | |
| α-helix | 259-293 | 35 | |
| α-helix | 294-298 | 5 | |
| α-helix | 305-333 | 29 | |
| α-helix | 336-348 | 13 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Guanine nucleotide-binding protein G(q) subunit alpha-1 | A | protein | 361 | Homo sapiens | |
| Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | B | protein | 344 | 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 | 128 | synthetic construct | |
| Bombesin receptor subtype-3 | R | protein | 399 | Homo sapiens | P32247 (AlphaFold model) |
Sequence of entity 1 (A), FASTA
>9M0J_1 Guanine nucleotide-binding protein G(q) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIEKQLQKDKQVYRRTLRLLLLGADNSGKSTIVKQMRIYHVNG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TSGIFETKFQVDKVNFHMFDVGAQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQEALNDF
KSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEPGEDPR
VTRAKYFIRKEFVDISTASGDGRHICYPHFTCSVDTENARRIFNDCKDIILQMNLREYNL
V
Sequence of entity 2 (B), FASTA
>9M0J_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
GSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLA
KIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGG
LDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQ
TTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFP
NGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNV
WDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN
Sequence of entity 3 (G), FASTA
>9M0J_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL
Sequence of entity 4 (N), FASTA
>9M0J_4 Nanobody-35 (chains N)
QVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVRQAPGKGLEWVSDISQSGASISY
TGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCARCPAPFTRDCFDVTSTTYAYRGQ
GTQVTVSS
Sequence of entity 5 (R), FASTA
>9M0J_5 Bombesin receptor subtype-3 (chains R)
MAQRQPHSPNQTLISITNDTESSSSVVSNDNTNKGWSGDNSPGIEALCAIYITYAVIISV
GILGNAILIKVFFKTKSMQTVPNIFITSLAFGDLLLLLTCVPVDATHYLAEGWLFGRIGC
KVLSFIRLTSVGVSVFTLTILSADRYKAVVKPLERQPSNAILKTCVKAGCVWIVSMIFAL
PEAIFSNVYTFRDPNKNMTFESCTSYPVSKKLLQEIHSLLCFLVFYIIPLSIISVYYSLI
ARTLYKSTLNIPTEEQSHARKQIESRKRIARTVLVLVALFALCWLPNHLLYLYHSFTSQT
YVDPSAMHFIFTIFSRVLAFSNSCVNPFALYWLSKSFQKHFKAQLFCCKAERPEPPVADT
SLTTLAVMGTVPGTGSIQMSEISVTSFTGCSVKQAEDRF
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ODN | (1beta,6beta,7beta,8alpha,9beta,10alpha,13alpha,14R,16beta)-1,6,7,14-tetrahydro… | C20 H30 O6 | 1 |
Primary citation
Cryo-EM structure of Bombesin receptor type-3 bound to oridonin. Li, C., Xu, Y., Yin, W. et al. To be published.
Other PDB entries of the same protein (UniProt P62873 (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
- 8F0K 1.9 Å, Human Amylin3 Receptor in complex with Gs and Pramlintide analogue peptide San385
- 9YDQ 1.94 Å, Human delta opioid receptor complex with mini-Gi and agonist DADLE and allosteric…
- 9YDP 1.95 Å, Human delta opioid receptor complex with mini-Gi and agonist DADLE
- 6CRK 2.0 Å, Heterotrimeric G-protein in complex with an antibody fragment
- 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
Browse structure collections
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