9CGK: Delta opioid receptor
CryoEM structure of delta opioid receptor bound to G proteins and a full bitopic agonist. Determined by electron microscopy at 2.62 Å resolution. Released 2 Apr 2025.
- Method
- Electron microscopy
- Resolution
- 2.62 Å
- Organisms
- Homo sapiens, Mus musculus
- Chains
- 5
- Atoms
- 8,480
- Mol. weight
- 146.46 kDa
- Ligands
- A1AWD
- Released
- 2 Apr 2025
Explore 9CGK in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9CGK contains 33 α-helices and 61 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: 14 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 46-77 | 32 | |
| α-helix | 83-99 | 17 | |
| α-helix | 102-111 | 10 | |
| α-helix | 117-151 | 35 | |
| α-helix | 153-159 | 7 | |
| α-helix | 162-185 | 24 | |
| β-strand | 187-190 | 4 | 1 |
| β-strand | 197-200 | 4 | 1 |
| α-helix | 203 | 1 | |
| α-helix | 206-218 | 13 | |
| α-helix | 219-223 | 5 | |
| α-helix | 224-242 | 19 | |
| α-helix | 252-256 | 5 | |
| α-helix | 257-286 | 30 | |
| α-helix | 294-321 | 28 | |
| α-helix | 323-327 | 5 | |
Chain B: 9 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-31 | 25 | |
| β-strand | 33-40 | 8 | 14 |
| β-strand | 185-190 | 6 | 14 |
| β-strand | 195-200 | 6 | 14 |
| α-helix | 208-210 | 3 | |
| α-helix | 212-215 | 4 | |
| β-strand | 220-226 | 7 | 14 |
| α-helix | 227-229 | 3 | |
| β-strand | 233 | 1 | 15 |
| β-strand | 241 | 1 | 15 |
| α-helix | 242-254 | 13 | |
| β-strand | 263-269 | 7 | 14 |
| α-helix | 271-277 | 7 | |
| α-helix | 296-309 | 14 | |
| β-strand | 319-323 | 5 | 14 |
| α-helix | 324-325 | 2 | |
| α-helix | 330-351 | 22 | |
Chain C: 4 helices, 28 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-24 | 21 | |
| α-helix | 30-34 | 5 | |
| α-helix | 38-40 | 3 | |
| α-helix | 45-46 | 2 | |
| β-strand | 47-51 | 5 | 7 |
| β-strand | 58-63 | 6 | 8 |
| β-strand | 69-74 | 6 | 8 |
| β-strand | 78-83 | 6 | 8 |
| β-strand | 88-94 | 7 | 8 |
| β-strand | 100-105 | 6 | 9 |
| β-strand | 111-116 | 6 | 9 |
| β-strand | 120-125 | 6 | 9 |
| β-strand | 134-140 | 7 | 9 |
| β-strand | 146-151 | 6 | 10 |
| β-strand | 156-161 | 6 | 10 |
| β-strand | 165-170 | 6 | 10 |
| β-strand | 175-181 | 7 | 10 |
| β-strand | 187-192 | 6 | 11 |
| β-strand | 198-203 | 6 | 11 |
| β-strand | 208-212 | 5 | 11 |
| β-strand | 218-222 | 5 | 11 |
| β-strand | 229-234 | 6 | 12 |
| β-strand | 240-245 | 6 | 12 |
| β-strand | 249-254 | 6 | 12 |
| β-strand | 259-265 | 7 | 12 |
| β-strand | 273-278 | 6 | 13 |
| β-strand | 284-289 | 6 | 13 |
| β-strand | 294-298 | 5 | 13 |
| β-strand | 303-308 | 6 | 13 |
| β-strand | 315-320 | 6 | 7 |
| β-strand | 327-331 | 5 | 7 |
| β-strand | 336-339 | 4 | 7 |
Chain D: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-23 | 14 | |
| α-helix | 30-43 | 14 | |
Chain E: 4 helices, 23 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-7 | 5 | 2 |
| β-strand | 10-12 | 3 | 3 |
| β-strand | 17-25 | 9 | 2 |
| α-helix | 29-31 | 3 | |
| β-strand | 33-39 | 7 | 3 |
| β-strand | 45-51 | 7 | 3 |
| β-strand | 58-60 | 3 | 3 |
| β-strand | 68-73 | 6 | 2 |
| β-strand | 78-84 | 7 | 2 |
| β-strand | 92-99 | 8 | 3 |
| β-strand | 111 | 1 | 3 |
| β-strand | 115-119 | 5 | 3 |
| β-strand | 128-129 | 2 | 4 |
| β-strand | 135-136 | 2 | 5 |
| β-strand | 143-149 | 7 | 4 |
| β-strand | 154 | 1 | 6 |
| β-strand | 160 | 1 | 6 |
| β-strand | 162-167 | 6 | 5 |
| β-strand | 174-177 | 4 | 5 |
| β-strand | 183 | 1 | 5 |
| α-helix | 184 | 1 | |
| β-strand | 191-196 | 6 | 4 |
| β-strand | 199-204 | 6 | 4 |
| α-helix | 209-211 | 3 | |
| β-strand | 213-219 | 7 | 5 |
| α-helix | 225 | 1 | |
| β-strand | 231-234 | 4 | 5 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Delta-type opioid receptor | A | protein | 303 | Homo sapiens | P41143 (AlphaFold model) |
| ScFv16 protein | E | protein | 251 | Mus musculus | |
| Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | D | protein | 71 | Homo sapiens | P59768 (AlphaFold model) |
| Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | C | protein | 340 | Homo sapiens | P62873 (AlphaFold model) |
| Guanine nucleotide-binding protein G(i) subunit alpha-1 | B | protein | 354 | Homo sapiens | P63096 (AlphaFold model) |
Sequence of entity 1 (A), FASTA
>9CGK_1 Delta-type opioid receptor (chains A)
GSPGARSASSLALAIAITALYSAVCAVGLLGNVLVMFGIVRYTKMKTATNIYIFNLALAD
ALATSTLPFQSAKYLMETWPFGELLCKAVLSIDYYNMFTSIFTLTMMSVDRYIAVCHPVK
ALDFRTPAKAKLINICIWVLASGVGVPIMVMAVTRPRDGAVVCMLQFPSPSWYWDTVTKI
CVFLFAFVVPILIITVCYGLMLLRLRSVRLLSGSKEKDRSLRRITRMVLVVVGAFVVCWA
PIHIFVIVWTLVDIDRRDPLVVAALHLCIALGYANSSLNPVLYAFLDENFKRCFRQLCRK
PCG
Sequence of entity 2 (E), FASTA
>9CGK_2 ScFv16 protein (chains E)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAA
Sequence of entity 3 (D), FASTA
>9CGK_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains D)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL
Sequence of entity 4 (C), FASTA
>9CGK_4 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains C)
GSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYA
MHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNI
CSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTF
TGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNA
FATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDAL
KADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN
Sequence of entity 5 (B), FASTA
>9CGK_5 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains B)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKNTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHASMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| A1AWD | N-{5-[(4bS,8R,8aS,15bR)-1,8a-dihydroxy-5,6,8,8a,9,15b-hexahydro-7H-4,8-methano[… | C29 H33 N5 O3 | 1 |
Primary citation
Structure-guided design of partial agonists at an opioid receptor. Varga, B.R., Bernhard, S.M., El Daibani, A. et al. Nat Commun (2025) 16:2518-2518. DOI 10.1038/s41467-025-57734-5 · PubMed
Other PDB entries of the same protein (UniProt P41143 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 4N6H 1.8 Å, 1.8 A Structure of the human delta opioid 7TM receptor (PSI Community Target)
- 9YDP 1.95 Å, Human delta opioid receptor complex with mini-Gi and agonist DADLE
- 4RWD 2.7 Å, XFEL structure of the human delta opioid receptor in complex with a bifunctional peptide
- 9XDQ 2.79 Å, Cryo-EM structure of BMS986187 bound DOR-Gi complex
- 6PT2 2.8 Å, Crystal structure of the active delta opioid receptor in complex with the peptide…
- 9CGJ 2.8 Å, CryoEM structure of delta opioid receptor bound to G proteins and a partial agonist
- 8Y71 2.97 Å, positive allosteric modulator(BMS986187)-bound delta-opioid receptor-Gi complex
- 8F7S 3.0 Å, Gi bound delta-opioid receptor in complex with deltorphin
- 9PPX 3.04 Å, CryoEM structure of delta opioid receptor bound to G proteins and naltrexone
- 9XF4 3.05 Å, Cryo-EM structure of Leu-enkephalin-BMS-986187-bound DOR-Gi2 complex
- 9PPY 3.1 Å, CryoEM structure of delta opioid receptor bound to G proteins and met-enkephalin
- 9PQ0 3.12 Å, CryoEM structure of delta opioid receptor bound to G proteins and ADL5859
Browse structure collections
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