8DZR: GR89,696 bound Kappa Opioid Receptor
GR89,696 bound Kappa Opioid Receptor in complex with gustducin. Determined by electron microscopy at 2.61 Å resolution. Released 3 May 2023.
- Method
- Electron microscopy
- Resolution
- 2.61 Å
- Organisms
- Homo sapiens, Mus musculus
- Chains
- 5
- Atoms
- 7,944
- Mol. weight
- 144.87 kDa
- Ligands
- U9I
- Released
- 3 May 2023
Explore 8DZR in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8DZR contains 32 α-helices and 63 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: 12 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 58-79 | 22 | |
| α-helix | 93-109 | 17 | |
| α-helix | 113-120 | 8 | |
| α-helix | 130-161 | 32 | |
| α-helix | 166-169 | 4 | |
| α-helix | 172-196 | 25 | |
| β-strand | 197-200 | 4 | 1 |
| β-strand | 209-212 | 4 | 1 |
| α-helix | 222-231 | 10 | |
| α-helix | 232-236 | 5 | |
| α-helix | 237-255 | 19 | |
| α-helix | 264-297 | 34 | |
| α-helix | 310-327 | 18 | |
| α-helix | 328-332 | 5 | |
Chain B: 8 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-30 | 24 | |
| β-strand | 33-39 | 7 | 2 |
| β-strand | 185-191 | 7 | 2 |
| β-strand | 194-200 | 7 | 2 |
| α-helix | 208-210 | 3 | |
| α-helix | 212-215 | 4 | |
| β-strand | 220-226 | 7 | 2 |
| α-helix | 243-254 | 12 | |
| β-strand | 263-269 | 7 | 2 |
| α-helix | 271-280 | 10 | |
| α-helix | 283-285 | 3 | |
| α-helix | 296-304 | 9 | |
| β-strand | 319-323 | 5 | 2 |
| α-helix | 331-351 | 21 | |
Chain C: 4 helices, 28 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-25 | 22 | |
| α-helix | 30-34 | 5 | |
| α-helix | 38-39 | 2 | |
| β-strand | 47-51 | 5 | 3 |
| β-strand | 58-63 | 6 | 4 |
| β-strand | 69-74 | 6 | 4 |
| β-strand | 78-83 | 6 | 4 |
| β-strand | 89-94 | 6 | 4 |
| α-helix | 95 | 1 | |
| β-strand | 100-105 | 6 | 5 |
| β-strand | 111-116 | 6 | 5 |
| β-strand | 120-125 | 6 | 5 |
| β-strand | 134-140 | 7 | 5 |
| β-strand | 146-151 | 6 | 6 |
| β-strand | 156-161 | 6 | 6 |
| β-strand | 165-170 | 6 | 6 |
| β-strand | 175-181 | 7 | 6 |
| β-strand | 187-192 | 6 | 7 |
| β-strand | 198-203 | 6 | 7 |
| β-strand | 208-212 | 5 | 7 |
| β-strand | 217-222 | 6 | 7 |
| β-strand | 229-234 | 6 | 8 |
| β-strand | 240-245 | 6 | 8 |
| β-strand | 250-254 | 5 | 8 |
| β-strand | 259-264 | 6 | 8 |
| β-strand | 273-278 | 6 | 9 |
| β-strand | 284-289 | 6 | 9 |
| β-strand | 294-298 | 5 | 9 |
| β-strand | 301-308 | 8 | 9 |
| β-strand | 315-320 | 6 | 3 |
| β-strand | 327-331 | 5 | 3 |
| β-strand | 336-339 | 4 | 3 |
Chain D: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 13-23 | 11 | |
| α-helix | 30-43 | 14 | |
| α-helix | 45-47 | 3 | |
Chain E: 5 helices, 27 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-7 | 5 | 10 |
| β-strand | 10-12 | 3 | 11 |
| β-strand | 17-25 | 9 | 10 |
| α-helix | 29-31 | 3 | |
| β-strand | 33-39 | 7 | 11 |
| β-strand | 45-51 | 7 | 11 |
| β-strand | 58-60 | 3 | 11 |
| β-strand | 68-73 | 6 | 10 |
| β-strand | 78-84 | 7 | 10 |
| α-helix | 88-90 | 3 | |
| β-strand | 92-99 | 8 | 11 |
| β-strand | 110-111 | 2 | 11 |
| β-strand | 115-119 | 5 | 11 |
| α-helix | 126-127 | 2 | |
| β-strand | 128 | 1 | 12 |
| β-strand | 129 | 1 | 13 |
| β-strand | 135-136 | 2 | 14 |
| β-strand | 143-148 | 6 | 13 |
| β-strand | 154 | 1 | 15 |
| β-strand | 160 | 1 | 15 |
| β-strand | 162-167 | 6 | 16 |
| β-strand | 174-177 | 4 | 16 |
| β-strand | 183 | 1 | 16 |
| α-helix | 184 | 1 | |
| β-strand | 191-196 | 6 | 13 |
| β-strand | 199-204 | 6 | 13 |
| β-strand | 214-219 | 6 | 16 |
| β-strand | 227 | 1 | 16 |
| β-strand | 228 | 1 | 12 |
| α-helix | 229-230 | 2 | |
| β-strand | 231-232 | 2 | 16 |
| β-strand | 233-234 | 2 | 14 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Kappa-type opioid receptor | A | protein | 287 | Homo sapiens | P41145 (AlphaFold model) |
| G alpha gustducin protein | B | protein | 354 | Homo sapiens | |
| Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | C | protein | 339 | Homo sapiens | P62873 (AlphaFold model) |
| Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | D | protein | 71 | Homo sapiens | P59768 (AlphaFold model) |
| ScFv16 protein | E | protein | 251 | Mus musculus | |
Sequence of entity 1 (A), FASTA
>8DZR_1 Kappa-type opioid receptor (chains A)
GSISPAIPVIITAVYSVVFVVGLVGNSLVMFVIIRYTKMKTATNIYIFNLALADALVTTT
MPFQSTVYLMNSWPFGDVLCKIVLSIDYYNMFTSIFTLTMMSVDRYIAVCHPVKALDFRT
PLKAKIINICIWLLSSSVGISAIVLGGTKVREDVDVIECSLQFPDDDYSWWDLFMKICVF
IFAFVIPVLIIIVCYTLMILRLKSVRLLSGSREKDRNLRRITRLVLVVVAVFVVCWTPIH
IFILVEALGSTSHSTAALSSYYFCIALGYTNSSLNPILYAFLDENFK
Sequence of entity 2 (B), FASTA
>8DZR_2 G alpha gustducin protein (chains B)
MGSTVSAEDKAAAERSKMIDKNLREDAERDARTVKLLLLGAGESGKATIVKQMKIIHKNG
YSEQECMEFKAVIYSNTLQSILAIVKAMTTLGIDYVNPRSAEDQRQLYAMANTLEDGGMT
PQLAEVIKRLWRDPGIQACFERASEYQLNDSAAYYLNDLDRITASGYVPNEQDVLHSRVK
TTGIIETQFSFKDLHFRMFDVGAQRSERKKWIHCFEGVTCIIFCAALSAYDMVLVEDEEV
NRMHASLKLFDSICNHKYFSDTSIVLFLNKKDIFQEKVTKVHLSICFPEYTGPNTFEDAG
NYIKNQFLDLNLKKEDKEIYSHMTCSTDTQNVKFVFDAVTDIIIKENLKDCGLF
Sequence of entity 3 (C), FASTA
>8DZR_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains C)
SELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAM
HWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNIC
SIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFT
GHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAF
ATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALK
ADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN
Sequence of entity 4 (D), FASTA
>8DZR_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains D)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL
Sequence of entity 5 (E), FASTA
>8DZR_5 ScFv16 protein (chains E)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| U9I | methyl (3R)-4-[(3,4-dichlorophenyl)acetyl]-3-[(pyrrolidin-1-yl)methyl]piperazin… | C19 H25 Cl2 N3 O3 | 1 |
Primary citation
Ligand and G-protein selectivity in the kappa-opioid receptor. Han, J., Zhang, J., Nazarova, A.L. et al. Nature (2023) 617:417-425. DOI 10.1038/s41586-023-06030-7 · PubMed
Other PDB entries of the same protein (UniProt P41145 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 7UL2 2.4 Å, CryoEM Structure of Inactive NTSR1 Bound to SR48692 and Nb6
- 22ES 2.43 Å, Gi bound kappa-opioid receptor in complex with difelikefalin
- 7T10 2.5 Å, CryoEM structure of somatostatin receptor 2 in complex with somatostatin-14 and Gi3
- 9PA4 2.5 Å, (S)-ketamine bound kappa-opioid receptor in complex with Gi1
- 8FEG 2.54 Å, CryoEM structure of Kappa Opioid Receptor bound to a semi-peptide and Gi1
- 9XDR 2.58 Å, Cryo-EM structure of asimadoline-BMS-986187-bound KOR-Gi1 complex
- 9ZZO 2.6 Å, MP1104-bound Kappa Opioid Receptor in complex with beta-arrestin1
- 9PA1 2.63 Å, PCP bound kappa-opioid receptor in complex with Gi1
- 8DZS 2.65 Å, GR89,696 bound Kappa Opioid Receptor in complex with Gz
- 7T11 2.7 Å, CryoEM structure of somatostatin receptor 2 in complex with Octreotide and Gi3.
- 8DZP 2.71 Å, momSalB bound Kappa Opioid Receptor in complex with Gi1
- 9V6O 2.76 Å, Cryo-EM structure of human kappa opioid receptor - G protein signaling complex bound…
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