9CGJ: Delta opioid receptor

CryoEM structure of delta opioid receptor bound to G proteins and a partial agonist. Determined by electron microscopy at 2.8 Å resolution. Released 2 Apr 2025.

Method: Electron microscopy
Resolution: 2.8 Å
Organisms: Homo sapiens, Mus musculus
Chains: 5
Atoms: 8,518
Mol. weight: 146.47 kDa
Ligands: A1AWC
Released: 2 Apr 2025

Explore 9CGJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9CGJ contains 35 α-helices and 62 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: 16 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	46-76	31
α-helix	83-98	16
α-helix	102-111	10
α-helix	117-151	35
α-helix	153-159	7
α-helix	162-175	14
α-helix	177-185	9
β-strand	189	1	1
β-strand	198	1	1
α-helix	202-203	2
α-helix	206-218	13
α-helix	219-223	5
α-helix	224-242	19
α-helix	251	1
α-helix	252-256	5
α-helix	257-286	30
α-helix	294-321	28
α-helix	323-327	5

Chain B: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-31	25
β-strand	34-40	7	7
α-helix	47-50	4
β-strand	185-191	7	7
β-strand	194-200	7	7
α-helix	208-210	3
α-helix	212-215	4
β-strand	220-226	7	7
β-strand	233	1	8
β-strand	241	1	8
α-helix	242-254	13
β-strand	263-269	7	7
α-helix	271-278	8
α-helix	296-308	13
β-strand	319-323	5	7
α-helix	331-350	20

Chain C: 3 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	3-25	23
α-helix	30-33	4
α-helix	34-36	3
β-strand	47-51	5	9
β-strand	58-63	6	10
β-strand	69-74	6	10
β-strand	78-83	6	10
β-strand	88-94	7	10
β-strand	100-105	6	11
β-strand	111-116	6	11
β-strand	121-125	5	11
β-strand	134-139	6	11
β-strand	146-151	6	12
β-strand	156-161	6	12
β-strand	165-170	6	12
β-strand	175-181	7	12
β-strand	187	1	13
β-strand	191-192	2	14
β-strand	198-202	5	14
β-strand	203	1	13
β-strand	208-212	5	14
β-strand	218-222	5	14
β-strand	229-234	6	15
β-strand	240-245	6	15
β-strand	250-254	5	15
β-strand	259-264	6	15
β-strand	273-278	6	16
β-strand	284-289	6	16
β-strand	294-298	5	16
β-strand	304-308	5	16
β-strand	315-320	6	9
β-strand	327-331	5	9
β-strand	336-339	4	9

Chain D: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	10-22	13
α-helix	30-42	13
α-helix	53-55	3

Chain E: 5 helices, 22 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
α-helix	62-64	3
β-strand	68-73	6	2
β-strand	78-84	7	2
α-helix	88-90	3
β-strand	92-99	8	3
β-strand	110-111	2	3
β-strand	115-119	5	3
β-strand	128-129	2	4
β-strand	143-149	7	4
β-strand	154	1	5
β-strand	160	1	5
β-strand	162-167	6	6
β-strand	173-177	5	6
α-helix	182	1
β-strand	183	1	6
α-helix	184	1
β-strand	191-196	6	4
β-strand	199-204	6	4
β-strand	213-219	7	6
β-strand	231-233	3	6

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) subunit alpha-1	B	protein	354	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	C	protein	340	Homo sapiens	P62873 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9CGJ_1 Delta-type opioid receptor (chains A)
GSPGARSASSLALAIAITALYSAVCAVGLLGNVLVMFGIVRYTKMKTATNIYIFNLALAD
ALATSTLPFQSAKYLMETWPFGELLCKAVLSIDYYNMFTSIFTLTMMSVDRYIAVCHPVK
ALDFRTPAKAKLINICIWVLASGVGVPIMVMAVTRPRDGAVVCMLQFPSPSWYWDTVTKI
CVFLFAFVVPILIITVCYGLMLLRLRSVRLLSGSKEKDRSLRRITRMVLVVVGAFVVCWA
PIHIFVIVWTLVDIDRRDPLVVAALHLCIALGYANSSLNPVLYAFLDENFKRCFRQLCRK
PCG

Sequence of entity 2 (E), FASTA

>9CGJ_2 ScFv16 protein (chains E)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAA

Sequence of entity 3 (D), FASTA

>9CGJ_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains D)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (B), FASTA

>9CGJ_4 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains B)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKNTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHASMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 5 (C), FASTA

>9CGJ_5 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains C)
GSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYA
MHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNI
CSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTF
TGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNA
FATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDAL
KADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Ligands and cofactors

ID	Name	Formula	Copies
A1AWC	N-{6-[(4bS,8R,8aS,15bR)-1,8a-dihydroxy-5,6,8,8a,9,15b-hexahydro-7H-4,8-methano[…	C30 H35 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
9CGK 2.62 Å, CryoEM structure of delta opioid receptor bound to G proteins and a full bitopic agonist
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…
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

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