7Y1F: Human k-opioid receptor-Gi complex

Cryo-EM structure of human k-opioid receptor-Gi complex. Determined by electron microscopy at 3.3 Å resolution. Released 24 May 2023.

Method: Electron microscopy
Resolution: 3.3 Å
Organism: Homo sapiens
Chains: 6
Atoms: 8,691
Mol. weight: 172.66 kDa
Released: 24 May 2023

Explore 7Y1F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7Y1F contains 30 α-helices and 65 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: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	12-31	20
β-strand	34-36	3	1
α-helix	46-52	7
β-strand	185-190	6	1
β-strand	195-200	6	1
α-helix	208-211	4
α-helix	213-215	3
β-strand	220	1	1
β-strand	223-226	4	2
α-helix	245-253	9
β-strand	261	1	1
β-strand	264-267	4	2
α-helix	274-280	7
α-helix	283-285	3
α-helix	296-310	15
β-strand	322-323	2	2
α-helix	331-344	14

Chain B: 5 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	6-24	19
α-helix	30-34	5
α-helix	38-39	2
β-strand	47-51	5	4
β-strand	58-63	6	5
β-strand	69	1	6
β-strand	70-74	5	5
β-strand	78-80	3	5
β-strand	83	1	6
β-strand	88	1	6
β-strand	92-94	3	5
β-strand	100-105	6	7
β-strand	111-116	6	7
β-strand	121-125	5	7
α-helix	133	1
β-strand	134-139	6	7
β-strand	146-153	8	8
β-strand	156-161	6	8
β-strand	166-170	5	8
β-strand	176-180	5	8
α-helix	186	1
β-strand	187-192	6	9
β-strand	198-203	6	9
β-strand	208-212	5	9
β-strand	221-222	2	9
β-strand	229-234	6	10
β-strand	240-245	6	10
β-strand	250-254	5	10
β-strand	260-264	5	10
β-strand	275-278	4	11
β-strand	284-288	5	11
β-strand	295-298	4	11
β-strand	304-307	4	11
β-strand	315-320	6	4
β-strand	327-331	5	4
β-strand	336-339	4	4

Chain C: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	10-23	14
α-helix	30-43	14
α-helix	54-55	2

Chain E: 2 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	10-12	3	13
β-strand	18-24	7	12
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	12
β-strand	78-83	6	12
α-helix	88-90	3
β-strand	92-99	8	13
β-strand	111	1	13
β-strand	115-119	5	13
β-strand	128-130	3	14
β-strand	134-135	2	15
β-strand	145-149	5	14
β-strand	154	1	16
β-strand	160	1	16
β-strand	162-167	6	15
β-strand	175-178	4	15
β-strand	182-183	2	15
β-strand	193-195	3	14
β-strand	199-202	4	14
β-strand	213-219	7	15
β-strand	227	1	15
β-strand	232-233	2	15

Chain R: 11 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	160-188	29
α-helix	195-211	17
α-helix	214-222	9
α-helix	230-263	34
α-helix	265-271	7
α-helix	274-297	24
β-strand	299-302	4	3
β-strand	311-314	4	3
α-helix	324-333	10
α-helix	334-338	5
α-helix	339-356	18
α-helix	365-398	34
α-helix	410-432	23

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)
Dynorphin	F	protein	13	Homo sapiens	P01213 (AlphaFold model)
Kappa-type opioid receptor	R	protein	460	Homo sapiens	P41145 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	351	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	protein	68	Homo sapiens	P59768
scFv16	E	protein	299	Homo sapiens

Sequence of entity 1 (A), FASTA

>7Y1F_1 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 2 (F), FASTA

>7Y1F_2 Dynorphin (chains F)
YGGFLRRIRPKLK

Sequence of entity 3 (R), FASTA

>7Y1F_3 Kappa-type opioid receptor (chains R)
MKTIIALSYIFCLVFADYKDDDDAKLQTMHHHHHHHHHHENLYFQGGTADLEDNWETLND
NLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQI
DDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLEISPAIPVIITAVYSVVFVVGLVGNS
LVMFVIIRYTKMKTATNIYIFNLALADALVTTTMPFQSTVYLMNSWPFGDVLCKIVLSID
YYNMFTSIFTLTMMSVDRYIAVCHPVKALDFRTPLKAKIINICIWLLSSSVGISAIVLGG
TKVREDVDVIECSLQFPDDDYSWWDLFMKICVFIFAFVIPVLIIIVCYTLMILRLKSVRL
LSGSREKDRNLRRITRLVLVVVAVFVVCWTPIHIFILVEALGSTSHSTAALSSYYFCIAL
GYTNSSLNPILYAFLDENFKRCFRDFCFPLKMRMERQSTS

Sequence of entity 4 (B), FASTA

>7Y1F_4 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRR
TLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSG
NYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALW
DIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDI
NAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGY
DDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 5 (C), FASTA

>7Y1F_5 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFC

Sequence of entity 6 (E), FASTA

>7Y1F_6 scFv16 (chains E)
GSMLLVNQSHQGFNKEHTSKMVSAIVLYVLLAAAAHSAFADVQLVESGGGLVQPGGSRKL
SCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYADTVKGRFTISRDDPKNTLF
LQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSSGGGGSGGGGSGGGGSDIVM
TQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVP
DRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFGAGTKLELKAAAHHHHHHHH

Primary citation

Cryo-EM structure of human kappa-opioid receptor-Gi complex bound to an endogenous agonist dynorphin A. Chen, Y., Chen, B., Wu, T. et al. Protein Cell (2023) 14:464-468. DOI 10.1093/procel/pwac033 · 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…

Browse structure collections

About this viewer

MolViewer shows 7Y1F directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.