8F7W: Gi bound kappa-opioid receptor

Gi bound kappa-opioid receptor in complex with dynorphin. Determined by electron microscopy at 3.19 Å resolution. Released 14 Dec 2022.

Method: Electron microscopy
Resolution: 3.19 Å
Organisms: Homo sapiens, Rattus norvegicus, Bos taurus
Chains: 6
Atoms: 9,087
Mol. weight: 158.53 kDa
Ligands: PLM, CLR
Released: 14 Dec 2022

Explore 8F7W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8F7W contains 38 α-helices and 64 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, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-31	25
β-strand	34-38	5	2
α-helix	47-54	8
β-strand	185-190	6	2
β-strand	195-200	6	2
α-helix	209-212	4
α-helix	213-215	3
β-strand	220-226	7	2
α-helix	228-230	3
α-helix	232	1
β-strand	233	1	3
α-helix	234	1
β-strand	241	1	3
α-helix	242-254	13
β-strand	263-269	7	2
α-helix	271-278	8
α-helix	296-308	13
β-strand	319-323	5	2
α-helix	331-351	21

Chain B: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	8-24	17
α-helix	30-33	4
α-helix	34-36	3
α-helix	38-39	2
β-strand	47-51	5	4
β-strand	60-63	4	5
β-strand	69-74	6	5
β-strand	78-83	6	5
β-strand	88-94	7	5
β-strand	100-105	6	6
β-strand	111-116	6	6
β-strand	121-125	5	6
β-strand	134-139	6	6
β-strand	146-151	6	7
β-strand	157-161	5	7
β-strand	165-169	5	7
β-strand	176-181	6	7
β-strand	187-192	6	8
β-strand	198-203	6	8
β-strand	208-212	5	8
β-strand	220-222	3	8
β-strand	229-234	6	9
β-strand	240-245	6	9
β-strand	250-254	5	9
β-strand	259-264	6	9
β-strand	273-278	6	10
β-strand	284-289	6	10
β-strand	294-298	5	10
β-strand	304-308	5	10
β-strand	315-320	6	4
β-strand	327-331	5	4
β-strand	336-339	4	4

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 E: 4 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	11
β-strand	11-12	2	12
β-strand	17-25	9	11
α-helix	29-31	3
β-strand	33-39	7	13
β-strand	45-51	7	13
β-strand	58-60	3	13
β-strand	68-73	6	11
β-strand	78-84	7	11
α-helix	88-90	3
β-strand	93-99	7	13
β-strand	111	1	13
β-strand	115-116	2	13
β-strand	118-119	2	12
β-strand	141-143	3	14
β-strand	147-149	3	15
β-strand	156-162	7	14
β-strand	167	1	16
β-strand	173	1	16
β-strand	175-180	6	15
β-strand	186-188	3	15
β-strand	190-191	2	17
β-strand	195-196	2	17
α-helix	197	1
β-strand	204-208	5	14
β-strand	212-217	6	14
α-helix	222-224	3
β-strand	227-232	6	15
β-strand	240	1	15
β-strand	244-247	4	15

Chain R: 15 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	58-82	25
α-helix	83-87	5
α-helix	93-109	17
α-helix	112-121	10
α-helix	128-161	34
α-helix	163-167	5
α-helix	172-196	25
β-strand	197-202	6	1
β-strand	207-212	6	1
α-helix	216-218	3
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
Kappa-type opioid receptor	R	protein	378	Homo sapiens	P41145 (AlphaFold model)
Dynorphin	P	protein	8	Homo sapiens	P01213 (AlphaFold model)
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	68	Bos taurus	P63212
scFv16	E	protein	248	synthetic construct

Sequence of entity 1 (R), FASTA

>8F7W_1 Kappa-type opioid receptor (chains R)
SPIQIFRGEPGPTCAPSACLPPNSSAWFPGWAEPDSNGSAGSEDAQLEPAHISPAIPVII
TAVYSVVFVVGLVGNSLVMFVIIRYTKMKTATNIYIFNLALADALVTTTMPFQSTVYLMN
SWPFGDVLCKIVISIDYYNMFTSIFTLTMMSVDRYIAVCHPVKALDFRTPLKAKIINICI
WLLSSSVGISAIVLGGTKVREDVDVIECSLQFPDDDYSWWDLFMKICVFIFAFVIPVLII
IVCYTLMILRLKSVRLLSGSREKDRNLRRITRLVLVVVAVFVVCWTPIHIFILVEALGST
SHSTAALSSYYFCIALGYTNSSLNPILYAFLDENFKRCFRDFCFPLKMRMERQSTSRVRN
TVQDPAYLRDIDGMNKPV

Sequence of entity 2 (P), FASTA

>8F7W_2 Dynorphin (chains P)
YGGFLRRI

Sequence of entity 3 (A), FASTA

>8F7W_3 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 4 (B), FASTA

>8F7W_4 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHHHGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRT
RRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAP
SGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCA
LWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHES
DINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLA
GYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 5 (C), FASTA

>8F7W_5 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFC

Sequence of entity 6 (E), FASTA

>8F7W_6 scFv16 (chains E)
MVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
AGGGGSGGGGSGGGGSADIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQ
RPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTF
GAGTKLEL

Ligands and cofactors

ID	Name	Formula	Copies
PLM	Palmitic acid	C16 H32 O2	2
CLR	Cholesterol	C27 H46 O	3

Primary citation

Structures of the entire human opioid receptor family. Wang, Y., Zhuang, Y., DiBerto, J.F. et al. Cell (2023) 186:413-427.e17. DOI 10.1016/j.cell.2022.12.026 · 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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