8FEG: Kappa Opioid Receptor

CryoEM structure of Kappa Opioid Receptor bound to a semi-peptide and Gi1. Determined by electron microscopy at 2.54 Å resolution. Released 6 Dec 2023.

Method: Electron microscopy
Resolution: 2.54 Å
Organisms: Homo sapiens, Mus musculus, synthetic construct
Chains: 6
Atoms: 8,539
Mol. weight: 150.63 kDa
Released: 6 Dec 2023

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

Secondary structure: helices and β-sheets

8FEG contains 36 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 B: 12 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	61-86	26
α-helix	93-109	17
α-helix	112-120	9
α-helix	128-161	34
α-helix	163-166	4
α-helix	172-194	23
β-strand	199-201	3	15
β-strand	208-210	3	15
α-helix	222-231	10
α-helix	232-236	5
α-helix	237-253	17
α-helix	263-298	36
α-helix	307-327	21
α-helix	328-332	5

Chain C: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-30	24
β-strand	34-39	6	1
β-strand	185-190	6	1
β-strand	195-200	6	1
α-helix	211-214	4
β-strand	220-226	7	1
α-helix	227-231	5
α-helix	242-254	13
β-strand	263-269	7	1
α-helix	271-280	10
α-helix	283-285	3
α-helix	296-308	13
β-strand	319-323	5	1
α-helix	330-350	21

Chain D: 6 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	3-25	23
α-helix	30-33	4
α-helix	34-36	3
α-helix	38-40	3
β-strand	47-51	5	2
α-helix	57	1
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	146-151	6	5
β-strand	156-161	6	5
β-strand	165-170	6	5
β-strand	176-181	6	5
β-strand	187-192	6	6
β-strand	198-203	6	6
β-strand	207-212	6	6
β-strand	217-223	7	6
β-strand	229-234	6	7
β-strand	240-245	6	7
β-strand	249-254	6	7
β-strand	259-265	7	7
α-helix	271-272	2
β-strand	273-278	6	8
β-strand	280	1	9
β-strand	282	1	9
β-strand	285-289	5	8
β-strand	294-297	4	8
β-strand	303	1	8
β-strand	308	1	8
β-strand	315-320	6	2
β-strand	327-331	5	2
β-strand	336-339	4	2

Chain E: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-17	9
α-helix	30-43	14
α-helix	45-47	3

Chain F: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	10-12	3	11
β-strand	18-25	8	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	78-83	6	10
α-helix	88-90	3
β-strand	92-99	8	11
β-strand	111	1	11
β-strand	115-119	5	11
α-helix	125-127	3
β-strand	128-129	2	12
β-strand	135-136	2	13
β-strand	143-149	7	12
β-strand	154	1	14
β-strand	160	1	14
β-strand	162-167	6	13
β-strand	173-177	5	13
β-strand	183	1	13
α-helix	184	1
β-strand	191-196	6	12
β-strand	199-204	6	12
α-helix	209-211	3
β-strand	213-219	7	13
α-helix	230	1
β-strand	231-234	4	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(i) subunit alpha-1	C	protein	354	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	D	protein	358	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	E	protein	71	Homo sapiens	P59768 (AlphaFold model)
scFv16 antibody fragment	F	protein	251	Mus musculus
Kappa-type opioid receptor	B	protein	308	Homo sapiens	P41145 (AlphaFold model)
Ace-tyr-ala-dty-thr-thr-cys-thr-dpn-XT9	A	protein	10	synthetic construct

Sequence of entity 1 (C), FASTA

>8FEG_1 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains C)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKNTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHASMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 2 (D), FASTA

>8FEG_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains D)
MHHHHHHLEVLFQGPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGR
IQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMT
CAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSG
DTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTF
TGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSG
RLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (E), FASTA

>8FEG_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains E)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (F), FASTA

>8FEG_4 scFv16 antibody fragment (chains F)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAA

Sequence of entity 5 (B), FASTA

>8FEG_5 Kappa-type opioid receptor (chains B)
LGSISPAIPVIITAVYSVVFVVGLVGNSLVMFVIIRYTKMKTATNIYIFNLALADALVTT
TMPFQSTVYLMNSWPFGDVLCKIVLSIDYYNMFTSIFTLTMMSVDRYIAVCHPVKALDFR
TPLKAKIINICIWLLSSSVGISAIVLGGTKVREDVDVIECSLQFPDDDYSWWDLFMKICV
FIFAFVIPVLIIIVCYTLMILRLKSVRLLSGSREKDRNLRRITRLVLVVVAVFVVCWTPI
HIFILVEALGSTSHSTAALSSYYFCIALGYTNSCLNPILYAFLDENFKRCFRDFCFPLKM
RMERQSTS

Sequence of entity 6 (A), FASTA

>8FEG_6 ACE-TYR-ALA-DTY-THR-THR-CYS-THR-DPN-XT9 (chains A)
XYAYTTCTFX

Primary citation

Design and structural validation of peptide-drug conjugate ligands of the kappa-opioid receptor. Muratspahic, E., Deibler, K., Han, J. et al. Nat Commun (2023) 14:8064. DOI 10.1016/0006-2952(73)90196-2 · 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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