8DZS: GR89,696 bound Kappa Opioid Receptor

GR89,696 bound Kappa Opioid Receptor in complex with Gz. Determined by electron microscopy at 2.65 Å resolution. Released 3 May 2023.

Method: Electron microscopy
Resolution: 2.65 Å
Organisms: Homo sapiens, Mus musculus
Chains: 5
Atoms: 8,245
Mol. weight: 147.02 kDa
Ligands: U9I
Released: 3 May 2023

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

Secondary structure: helices and β-sheets

8DZS contains 35 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	61-64	4
α-helix	65-86	22
α-helix	93-109	17
α-helix	113-120	8
α-helix	128-161	34
α-helix	166-169	4
α-helix	172-195	24
β-strand	199-201	3	1
β-strand	208-210	3	1
α-helix	221-223	3
α-helix	228-231	4
α-helix	232-236	5
α-helix	237-253	17
α-helix	265-299	35
α-helix	307-327	21
α-helix	328-332	5

Chain B: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-31	25
β-strand	33-38	6	2
α-helix	46-51	6
β-strand	186-191	6	2
β-strand	196-201	6	2
α-helix	209-211	3
α-helix	213-216	4
β-strand	221-227	7	2
α-helix	243-255	13
β-strand	264-270	7	2
α-helix	272-278	7
α-helix	300-310	11
β-strand	320-324	5	2
α-helix	331-351	21

Chain C: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	5-24	20
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	88-94	7	4
α-helix	95	1
β-strand	100-105	6	5
β-strand	111-116	6	5
β-strand	120-125	6	5
α-helix	129-131	3
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	303-308	6	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
α-helix	12-21	10
α-helix	30-43	14
α-helix	53-55	3

Chain E: 5 helices, 25 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
α-helix	53-55	3
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	113	1	10
β-strand	115-119	5	11
β-strand	129	1	12
β-strand	134-136	3	13
β-strand	143-148	6	12
β-strand	154	1	14
β-strand	160	1	14
β-strand	162-167	6	13
β-strand	174-178	5	13
β-strand	182-183	2	13
α-helix	184	1
β-strand	191-196	6	12
β-strand	199-204	6	12
β-strand	213-219	7	13
α-helix	225	1
β-strand	227	1	13
β-strand	231-234	4	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Kappa-type opioid receptor	A	protein	308	Homo sapiens	P41145 (AlphaFold model)
Guanine nucleotide-binding protein G(z) subunit alpha	B	protein	349	Homo sapiens	P19086 (AlphaFold model)
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

>8DZS_1 Kappa-type opioid receptor (chains A)
LGSISPAIPVIITAVYSVVFVVGLVGNSLVMFVIIRYTKMKTATNIYIFNLALADALVTT
TMPFQSTVYLMNSWPFGDVLCKIVLSIDYYNMFTSIFTLTMMSVDRYIAVCHPVKALDFR
TPLKAKIINICIWLLSSSVGISAIVLGGTKVREDVDVIECSLQFPDDDYSWWDLFMKICV
FIFAFVIPVLIIIVCYTLMILRLKSVRLLSGSREKDRNLRRITRLVLVVVAVFVVCWTPI
HIFILVEALGSTSHSTAALSSYYFCIALGYTNSSLNPILYAFLDENFKRCFRDFCFPLKM
RMERQSTS

Sequence of entity 2 (B), FASTA

>8DZS_2 Guanine nucleotide-binding protein G(z) subunit alpha (chains B)
MGSTVSAEDKAAAERSKMIDKNLREDGEKQRREIKLLLLGTSNSGKNTIVKQMKIIHSGG
FNLEACKEYKPLIIYNAIDSLTRIIRALAALRIDFHNPDRAYDAVQLFALTGPAESKGEI
TPELLGVMRRLWADPGAQACFSRSSEYHLEDNAAYYLNDLERIAAADYIPTVEDILRSRD
MTTGIVENKFTFKELTFKMVDVGAQRSERKKWIHCFEGVTAIIFCVELSGYDLQTSRMAA
SLKLFDSICNNKWFIDTSLILFLNKKDLLAEKIRRIPLTICFPEYKGQNTYEEAAVYIQR
QFEDLNRNKETKEIYSHFTCSTDTSNIQFVFDAVTDVIIQNNLKYIGLC

Sequence of entity 3 (C), FASTA

>8DZS_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

>8DZS_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains D)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 5 (E), FASTA

>8DZS_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
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
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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