9L60: Gi-bound kappa opioid receptor

Gi-bound kappa opioid receptor in complex with dynorphin and positive allosteric modulator MPAM-15. Determined by electron microscopy at 2.9 Å resolution. Released 31 Dec 2025.

Method: Electron microscopy
Resolution: 2.9 Å
Organisms: Homo sapiens, Rattus norvegicus, Bos taurus
Chains: 5
Atoms: 7,260
Mol. weight: 134.94 kDa
Ligands: A1D6C, CLR
Released: 31 Dec 2025

Explore 9L60 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9L60 contains 35 α-helices and 38 β-strands across 4 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, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-30	24
β-strand	34-40	7	1
α-helix	47-54	8
β-strand	185-190	6	1
β-strand	195-200	6	1
α-helix	208-210	3
α-helix	212-215	4
β-strand	220-226	7	1
α-helix	227-230	4
α-helix	232	1
β-strand	233	1	2
α-helix	234	1
β-strand	241	1	2
α-helix	242-254	13
β-strand	263-269	7	1
α-helix	271-278	8
α-helix	283-285	3
α-helix	296-308	13
β-strand	319-323	5	1
α-helix	331-351	21

Chain B: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	76-93	18
α-helix	98-101	4
α-helix	102-104	3
α-helix	106-107	2
β-strand	117-120	4	3
β-strand	126-131	6	4
β-strand	137-142	6	4
β-strand	146-151	6	4
β-strand	156-162	7	4
β-strand	168-173	6	5
β-strand	179-184	6	5
β-strand	189-193	5	5
β-strand	202-207	6	5
β-strand	214-219	6	6
β-strand	225-229	5	6
β-strand	233-237	5	6
β-strand	244-249	6	6
β-strand	255-260	6	7
β-strand	266-271	6	7
β-strand	276-280	5	7
β-strand	286-290	5	7
β-strand	297-302	6	8
β-strand	308-313	6	8
β-strand	318-322	5	8
β-strand	327-332	6	8
α-helix	340	1
β-strand	341-346	6	9
β-strand	352-357	6	9
β-strand	361-366	6	9
β-strand	372-377	6	9
β-strand	383-387	5	3
β-strand	396-399	4	3
β-strand	403-406	4	3

Chain C: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	10-23	14
α-helix	30-43	14
α-helix	45-47	3
α-helix	53-55	3

Chain D: 14 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	58-82	25
α-helix	83-87	5
α-helix	93-110	18
α-helix	112-121	10
α-helix	128-161	34
α-helix	163-166	4
α-helix	172-196	25
β-strand	197-202	6	10
β-strand	207-212	6	10
α-helix	219-231	13
α-helix	232-236	5
α-helix	237-254	18
α-helix	263-295	33
α-helix	296-300	5
α-helix	306-330	25
α-helix	335-341	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	354	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	353	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)
Kappa-type opioid receptor	D	protein	397	Homo sapiens	P41145 (AlphaFold model)
Dynorphin A(1-13)	P	protein	13	Homo sapiens	P01213

Sequence of entity 1 (A), FASTA

>9L60_1 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 2 (B), FASTA

>9L60_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHHHGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRT
RRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAP
SGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCA
LWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHES
DINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLA
GYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (C), FASTA

>9L60_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (D), FASTA

>9L60_4 Kappa-type opioid receptor (chains D)
DYKDDDDVDASSPIQIFRGEPGPTCAPSACLPPNSSAWFPGWAEPDSNGSAGSEDAQLEP
AHISPAIPVIITAVYSVVFVVGLVGNSLVMFVIIRYTKMKTATNIYIFNLALADALVTTT
MPFQSTVYLMNSWPFGDVLCKIVISIDYYNMFTSIFTLTMMSVDRYIAVCHPVKALDFRT
PLKAKIINICIWLLSSSVGISAIVLGGTKVREDVDVIECSLQFPDDDYSWWDLFMKICVF
IFAFVIPVLIIIVCYTLMILRLKSVRLLSGSREKDRNLRRITRLVLVVVAVFVVCWTPIH
IFILVEALGSTSHSTAALSSYYFCIALGYTNSSLNPILYAFLDENFKRCFRDFCFPLKMR
MERQSTSRVRNTVQDPAYLRDIDGMNKPVHHHHHHHH

Sequence of entity 5 (P), FASTA

>9L60_5 Dynorphin A(1-13) (chains P)
YGGFLRRIRPKLK

Ligands and cofactors

ID	Name	Formula	Copies
A1D6C	9-[5-(3-chlorophenyl)furan-2-yl]-3,3,6,6-tetramethyl-4,5,7,9-tetrahydro-2~{H}-x…	C27 H27 Cl O4	1
CLR	Cholesterol	C27 H46 O	2

Primary citation

Structure-based design of an opioid receptor modulator for enhanced morphine analgesia. Wang, Y., Luo, P., Xu, H. et al. Sci Adv (2026) 12:eaea9832-eaea9832. DOI 10.1126/sciadv.aea9832 · PubMed

Other PDB entries of the same protein (UniProt P63096 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6CRK 2.0 Å, Heterotrimeric G-protein in complex with an antibody fragment
3UMR 2.04 Å, Crystal structure of the G202D mutant of human G-alpha-i1
9P7Z 2.1 Å, NTSR1-Gi-NTS(8-13) Complex in the Canonical, AHD Open State (C-Open-Apo)
2OM2 2.2 Å, Crystal Structure Of Human G[alpha]i1 Bound To The Goloco Motif Of Rgs14
8YN9 2.3 Å, Cryo-EM structure of histamine H4 receptor in complex with histamine and Gi
9HYI 2.3 Å, DP81-bound serotonin 5-HT1A receptor - Gi Protein Complex
9O36 2.3 Å, CryoEM structure of mu-opioid receptor - Gi protein complex bound to fluornitrazene (FNZ)
9P80 2.3 Å, NTSR1-Gi-NTS(8-13) Complex in the Non-Canonical, AHD Open State (NC-Open-Apo)
8XXV 2.33 Å, Cryo-EM Structure of the Prostaglandin D2 Receptor 2-indomethacin Coupled to G Protein
3UMS 2.34 Å, Crystal structure of the G202A mutant of human G-alpha-i1
3ONW 2.38 Å, Structure of a G-alpha-i1 mutant with enhanced affinity for the RGS14 GoLoco motif.
20ZG 2.4 Å, Cryo-EM structure of the human neurotensin receptor 1 (hNTSR1)-Gi1 complex in the…

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