8VVF: Kappa opioid receptor:Galphai protein

Kappa opioid receptor:Galphai protein in complex with inverse agonist JDTic. Determined by electron microscopy at 3.0 Å resolution. Released 15 Jan 2025.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Homo sapiens, Mus musculus
Chains: 5
Atoms: 8,581
Mol. weight: 155.52 kDa
Ligands: JDC
Released: 15 Jan 2025

Explore 8VVF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8VVF contains 29 α-helices and 67 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: 11 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	58-86	29
α-helix	93-109	17
α-helix	111-121	11
α-helix	131-160	30
α-helix	163-169	7
α-helix	172-195	24
β-strand	197-201	5	1
β-strand	208-212	5	1
α-helix	220-235	16
α-helix	237-255	19
α-helix	265-299	35
α-helix	306-332	27
α-helix	336-341	6

Chain B: 9 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	7-27	21
α-helix	29-32	4
β-strand	36	1	10
β-strand	37-39	3	11
α-helix	184	1
β-strand	185-189	5	10
β-strand	196-200	5	10
α-helix	208-210	3
α-helix	212-214	3
β-strand	220-226	7	11
α-helix	242-254	13
β-strand	263-269	7	11
α-helix	271-276	6
α-helix	296-308	13
β-strand	319-323	5	11
α-helix	332-351	20

Chain C: 3 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	3-25	23
α-helix	31-34	4
α-helix	38-40	3
β-strand	47-50	4	2
β-strand	58-63	6	3
β-strand	69-74	6	3
β-strand	78-83	6	3
β-strand	89-94	6	3
β-strand	100-105	6	4
β-strand	111-116	6	4
β-strand	120-125	6	4
β-strand	134-140	7	4
β-strand	146-148	3	5
β-strand	151	1	5
β-strand	156-161	6	5
β-strand	165-170	6	5
β-strand	176-181	6	5
β-strand	187	1	6
β-strand	191-192	2	7
β-strand	198-202	5	7
β-strand	203	1	6
β-strand	207-212	6	7
β-strand	218-223	6	7
β-strand	229-234	6	8
β-strand	240-245	6	8
β-strand	250-254	5	8
β-strand	262-264	3	8
β-strand	276-278	3	9
β-strand	284-288	5	9
β-strand	294-298	5	9
β-strand	304-307	4	9
β-strand	315-320	6	2
β-strand	327-331	5	2
β-strand	336-339	4	2

Chain D: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	9-23	15
α-helix	30-43	14

Chain E: 4 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	10-12	3	13
β-strand	17-24	8	12
α-helix	29-31	3
β-strand	34-39	6	14
β-strand	45-51	7	14
α-helix	53-55	3
β-strand	58-60	3	14
β-strand	68-73	6	12
β-strand	78-84	7	12
α-helix	88-90	3
β-strand	92-94	3	13
β-strand	95-98	4	14
β-strand	110-111	2	14
β-strand	115-119	5	13
β-strand	128-129	2	15
β-strand	135-136	2	16
β-strand	144-149	6	15
β-strand	154	1	17
β-strand	160	1	17
β-strand	162-167	6	18
β-strand	173-177	5	18
β-strand	191	1	19
β-strand	194	1	15
β-strand	199-203	5	15
β-strand	204	1	19
α-helix	209-211	3
β-strand	214-219	6	18
β-strand	227	1	18
β-strand	231-232	2	18
β-strand	233-234	2	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Kappa-type opioid receptor	A	protein	380	Homo sapiens	P41145 (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)/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)
scFv16	E	protein	251	Mus musculus

Sequence of entity 1 (A), FASTA

>8VVF_1 Kappa-type opioid receptor (chains A)
MDSPIQIFRGEPGPTCAPSACLPPNSSAWFPGWAEPDSNGSAGSEDAQLEPAHISPAIPV
IITAVYSVVFVVGLVGNSLVMFVIIRYTKMKTATNIYIFNLALADALVTTTMPFQSTVYL
MNSWPFGDVLCKIVISIDYYNMFTSIFTLTMMSVDRYIAVCHPVKALDFRTPLKAKIINI
CIWLLSSSVGISAIVLGGTKVREDVDVIECSLQFPDDDYSWWDLFMKICVFIFAFVIPVL
IIIVCYTLMILRLKSVRLLSGSREKDRNLRRITRLVLVVVAVFVVCWTPIHIFILVEALG
STSHSTAALSSYYFCIALGYTNSSLNPILYAFLDENFKRCFRDFCFPLKMRMERQSTSRV
RNTVQDPAYLRDIDGMNKPV

Sequence of entity 2 (C), FASTA

>8VVF_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains C)
MSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYA
MHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNI
CSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTF
TGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNA
FATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDAL
KADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (D), FASTA

>8VVF_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains D)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (B), FASTA

>8VVF_4 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains B)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 5 (E), FASTA

>8VVF_5 scFv16 (chains E)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAA

Ligands and cofactors

ID	Name	Formula	Copies
JDC	(3R)-7-hydroxy-N-{(2S)-1-[(3R,4R)-4-(3-hydroxyphenyl)-3,4-dimethylpiperidin-1-y…	C28 H39 N3 O3	1

Primary citation

Molecular mechanisms of inverse agonism via kappa-opioid receptor-G protein complexes. Tyson, A.S., Khan, S., Motiwala, Z. et al. Nat Chem Biol (2025) 21:1046-1057. DOI 10.1038/s41589-024-01812-0 · 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
8DZR 2.61 Å, GR89,696 bound Kappa Opioid Receptor in complex with gustducin
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

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