8DZQ: MomSalB bound Kappa Opioid Receptor

momSalB bound Kappa Opioid Receptor in complex with GoA. Determined by electron microscopy at 2.82 Å resolution. Released 3 May 2023.

Method: Electron microscopy
Resolution: 2.82 Å
Organisms: Homo sapiens, Mus musculus
Chains: 5
Atoms: 8,342
Mol. weight: 147.27 kDa
Ligands: U99
Released: 3 May 2023

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

Secondary structure: helices and β-sheets

8DZQ contains 30 α-helices and 63 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: 13 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	58-86	29
α-helix	88-90	3
α-helix	93-109	17
α-helix	112-121	10
α-helix	128-161	34
α-helix	166-169	4
α-helix	172-196	25
β-strand	198-200	3	16
β-strand	209-211	3	16
α-helix	224-231	8
α-helix	232-236	5
α-helix	237-254	18
α-helix	266-298	33
α-helix	307-327	21
α-helix	328-332	5

Chain B: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-30	24
β-strand	33-39	7	15
α-helix	47-52	6
β-strand	186-192	7	15
β-strand	195-201	7	15
α-helix	213-216	4
β-strand	221-227	7	15
α-helix	229-231	3
α-helix	246-248	3
α-helix	252-255	4
β-strand	264-270	7	15
α-helix	272-276	5
α-helix	297-309	13
β-strand	319-323	5	15
α-helix	332-350	19

Chain C: 2 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	6-24	19
β-strand	47-51	5	1
β-strand	58-63	6	2
β-strand	69-74	6	2
β-strand	78-83	6	2
β-strand	88-94	7	2
β-strand	100-105	6	3
β-strand	111-116	6	3
β-strand	120-125	6	3
α-helix	129-131	3
β-strand	134-140	7	3
β-strand	146-151	6	4
β-strand	156-161	6	4
β-strand	165-170	6	4
β-strand	176-181	6	4
β-strand	187	1	5
β-strand	191-192	2	6
β-strand	198-202	5	6
β-strand	203	1	5
β-strand	208-212	5	6
β-strand	218-222	5	6
β-strand	229-234	6	7
β-strand	240-245	6	7
β-strand	249-254	6	7
β-strand	260-265	6	7
β-strand	273-278	6	8
β-strand	284-289	6	8
β-strand	294-298	5	8
β-strand	304-308	5	8
β-strand	315-320	6	1
β-strand	327-331	5	1
β-strand	336-339	4	1

Chain D: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	13-23	11
α-helix	30-43	14
α-helix	45-47	3

Chain E: 3 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	10-12	3	10
β-strand	18-25	8	9
α-helix	29-31	3
β-strand	33-39	7	10
β-strand	45-51	7	10
α-helix	53-55	3
β-strand	58-60	3	10
β-strand	68-73	6	9
β-strand	78-83	6	9
β-strand	92-99	8	10
β-strand	111	1	10
β-strand	113	1	9
β-strand	115-119	5	10
β-strand	128-129	2	11
β-strand	134-136	3	12
β-strand	143-147	5	13
β-strand	148-149	2	11
β-strand	154	1	14
β-strand	160	1	14
β-strand	162-167	6	12
β-strand	174-178	5	12
β-strand	182-183	2	12
β-strand	191-196	6	13
β-strand	199-204	6	13
β-strand	213-219	7	12
α-helix	225	1
β-strand	231-234	4	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
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
Guanine nucleotide-binding protein G(o) subunit alpha	B	protein	354	Homo sapiens	P09471 (AlphaFold model)
Kappa-type opioid receptor	A	protein	308	Homo sapiens	P41145 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>8DZQ_1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains C)
SELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAM
HWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNIC
SIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFT
GHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAF
ATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALK
ADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 2 (D), FASTA

>8DZQ_2 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains D)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 3 (E), FASTA

>8DZQ_3 ScFv16 protein (chains E)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAA

Sequence of entity 4 (B), FASTA

>8DZQ_4 Guanine nucleotide-binding protein G(o) subunit alpha (chains B)
MGSTLSAEERAALERSKAIEKNLKEDGISAAKDVKLLLLGAGESGKNTIVKQMKIIHEDG
FSGEDVKQYKPVVYSNTIQSLAAIVRAMDTLGIEYGDKERKADAKMVCDVVSRMEDTEPF
SAELLSAMMRLWGDSGIQECFNRSREYQLNDSAKYYLDSLDRIGAADYQPTEQDILRTRV
KTTGIVETHFTFKNLHFRLFDVGAQRSERKKWIHCFEDVTAIIFCVALSGYDQVLHEDET
TNRMHASLKLFDSICNNKFFIDTSIILFLNKKDLFGEKIKKSPLTICFPEYTGPNTYEDA
AAYIQAQFESKNRSPNKEIYCHMTCSTDTNNIQVVFDAVTDIIIANNLRGCGLY

Sequence of entity 5 (A), FASTA

>8DZQ_5 Kappa-type opioid receptor (chains A)
LGSISPAIPVIITAVYSVVFVVGLVGNSLVMFVIIRYTKMKTATNIYIFNLALADALVTT
TMPFQSTVYLMNSWPFGDVLCKIVLSIDYYNMFTSIFTLTMMSVDRYIAVCHPVKALDFR
TPLKAKIINICIWLLSSSVGISAIVLGGTKVREDVDVIECSLQFPDDDYSWWDLFMKICV
FIFAFVIPVLIIIVCYTLMILRLKSVRLLSGSREKDRNLRRITRLVLVVVAVFVVCWTPI
HIFILVEALGSTSHSTAALSSYYFCIALGYTNSSLNPILYAFLDENFKRCFRDFCFPLKM
RMERQSTS

Ligands and cofactors

ID	Name	Formula	Copies
U99	methyl (2S,4aR,6aR,7R,9S,10aS,10bR)-2-(furan-3-yl)-9-(methoxymethoxy)-6a,10b-di…	C23 H30 O8	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 P62873 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8QEH 1.43 Å, Crystal structure of the G11 protein heterotrimer bound to FR900359 inhibitor
8QEG 1.7 Å, Crystal structure of the G11 protein heterotrimer bound to YM-254890 inhibitor
8F0K 1.9 Å, Human Amylin3 Receptor in complex with Gs and Pramlintide analogue peptide San385
9YDQ 1.94 Å, Human delta opioid receptor complex with mini-Gi and agonist DADLE and allosteric…
9YDP 1.95 Å, Human delta opioid receptor complex with mini-Gi and agonist DADLE
6CRK 2.0 Å, Heterotrimeric G-protein in complex with an antibody fragment
8F0J 2.0 Å, Calcitonin Receptor in complex with Gs and Pramlintide analogue peptide San45
8F2B 2.0 Å, Amylin 3 Receptor in complex with Gs and Pramlintide analogue peptide San45
9XXT 2.0 Å, Cryo-EM structure of lysophosphatidylserine (18:0)-bound GPR174-Gs complex
6X18 2.1 Å, GLP-1 peptide hormone bound to Glucagon-Like peptide-1 (GLP-1) Receptor
6X19 2.1 Å, Non peptide agonist CHU-128, bound to Glucagon-Like peptide-1 (GLP-1) Receptor
9NTU 2.1 Å, Cryo-EM structure of BETP-GLP-1(9-36)-GLP-1R-Gs complex

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