9K07: DSO-5a-bound human BRS3-Gq complex

Cryo-EM structure of the DSO-5a-bound human BRS3-Gq complex. Determined by electron microscopy at 2.83 Å resolution. Released 27 Aug 2025.

Method: Electron microscopy
Resolution: 2.83 Å
Organisms: Homo sapiens, Oplophorus gracilirostris, Mus musculus
Chains: 6
Atoms: 9,618
Mol. weight: 185.64 kDa
Ligands: A1EL6
Released: 27 Aug 2025

Explore 9K07 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9K07 contains 29 α-helices and 72 β-strands across 6 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: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	7-30	24
β-strand	33-38	6	1
β-strand	69-76	8	1
β-strand	79-86	8	1
α-helix	96-101	6
β-strand	105-111	7	1
α-helix	118-130	13
β-strand	138-144	7	1
α-helix	146-155	10
α-helix	160-163	4
α-helix	165-167	3
α-helix	184-202	19
β-strand	211	1	1
β-strand	214-215	2	1
α-helix	223-242	20

Chain B: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-25	22
α-helix	30-33	4
α-helix	38-39	2
β-strand	47-51	5	8
β-strand	58-63	6	9
β-strand	69-74	6	9
β-strand	78-83	6	9
β-strand	88-94	7	9
β-strand	100-105	6	10
β-strand	111-116	6	10
β-strand	121-125	5	10
β-strand	134-139	6	10
β-strand	146-151	6	11
β-strand	156-161	6	11
β-strand	165-170	6	11
β-strand	175-181	7	11
β-strand	187-192	6	12
β-strand	198-203	6	12
β-strand	207-212	6	12
β-strand	218-223	6	12
β-strand	229-234	6	13
β-strand	240-245	6	13
β-strand	250-254	5	13
β-strand	259-264	6	13
α-helix	272	1
β-strand	273-278	6	14
β-strand	284-289	6	14
β-strand	294-298	5	14
β-strand	303-307	5	14
β-strand	315-320	6	8
β-strand	327-331	5	8
β-strand	336-339	4	8

Chain E: 2 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	2
β-strand	9-11	3	3
β-strand	16-24	9	2
α-helix	28-30	3
β-strand	32-38	7	4
β-strand	44-50	7	4
β-strand	57-59	3	4
β-strand	67-72	6	2
β-strand	77-83	7	2
β-strand	91-93	3	3
β-strand	94-98	5	4
β-strand	109-110	2	4
β-strand	114-118	5	3
β-strand	140-141	2	5
β-strand	146-148	3	6
β-strand	155-161	7	5
β-strand	166	1	7
β-strand	172	1	7
β-strand	174-179	6	6
β-strand	185-190	6	6
β-strand	194-195	2	6
β-strand	203-207	5	5
β-strand	211-216	6	5
α-helix	221-223	3
β-strand	225-231	7	6
β-strand	239	1	6
β-strand	243-246	4	6

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	8-23	16
α-helix	30-43	14
α-helix	53-55	3

Chain N: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	15
β-strand	11	1	16
β-strand	17-25	9	15
α-helix	29-31	3
β-strand	34-39	6	17
β-strand	45-51	7	17
β-strand	58-60	3	17
β-strand	68-73	6	15
β-strand	78-84	7	15
α-helix	88-90	3
β-strand	92-98	7	17
β-strand	118	1	17
β-strand	122-124	3	17
β-strand	125	1	16

Chain R: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	51-74	24
α-helix	81-106	26
α-helix	119-150	32
α-helix	161-178	18
α-helix	213-222	10
α-helix	223-227	5
α-helix	228-250	23
α-helix	259-296	38
α-helix	307-333	27
α-helix	335-344	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Bombesin receptor subtype-3,Oplophorus-luciferin 2-monooxygenase catalytic subunit	R	protein	612	Homo sapiens, Oplophorus gracilirostris	P32247 (AlphaFold model), Q9GV45 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-2,Guanine nucleotide-binding protein G(s)…	A	protein	246	Homo sapiens	P63092 (AlphaFold model)
scFv16	E	protein	267	Mus musculus
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	345	Rattus norvegicus	P54311 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	70	Bos taurus	P63212
Nanobody-35	N	protein	140	Lama glama

Sequence of entity 1 (R), FASTA

>9K07_1 Bombesin receptor subtype-3,Oplophorus-luciferin 2-monooxygenase catalytic subunit (chains R)
MKTIIALSYIFCLVFAMAQRQPHSPNQTLISITNDTESSSSVVSNDNTNKGWSGDNSPGI
EALCAIYITYAVIISVGILGNAILIKVFFKTKSMQTVPNIFITSLAFGDLLLLLTCVPVD
ATHYLAEGWLFGRIGCKVLSFIRLTSVGVSVFTLTILSADRYKAVVKPLERQPSNAILKT
CVKAGCVWIVSMIFALPEAIFSNVYTFRDPNKNMTFESCTSYPVSKKLLQEIHSLLCFLV
FYIIPLSIISVYYSLIARTLYKSTLNIPTEEQSHARKQIESRKRIARTVLVLVALFALCW
LPNHLLYLYHSFTSQTYVDPSAMHFIFTIFSRVLAFSNSCVNPFALYWLSKSFQKHFKAQ
LFCCKAERPEPPVADTSLTTLAVMGTVPGTGSIQMSEISVTSFTGCSVKQAEDRFGSSGG
GGSGGGGSSGVFTLEDFVGDWEQTAAYNLDQVLEQGGVSSLLQNLAVSVTPIQRIVRSGE
NALKIDIHVIIPYEGLSADQMAQIEEVFKVVYPVDDHHFKVILPYGTLVIDGVTPNMLNY
FGRPYEGIAVFDGKKITVTGTLWNGNKIIDERLITPDGSMLFRVTINSGGSENLYFQGGS
AGSAHHHHHHHH

Sequence of entity 2 (A), FASTA

>9K07_2 Guanine nucleotide-binding protein G(i) subunit alpha-2,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short (chains A)
MGSTVSAEDKAAAERSKMIDKNLREDGEKARRTLRLLLLGADNSGKSTIVKQMRILHGGS
GGSGGTSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQE
ALNDFKSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEP
GEDPRVTRAKYFIRKEFVDISTASGDGRHICYPHFTCAVDTENARRIFNDCKDIILQMNL
REYNLV

Sequence of entity 3 (E), FASTA

>9K07_3 scFv16 (chains E)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAALEVLFQGPHHHHHHHH

Sequence of entity 4 (B), FASTA

>9K07_4 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHL
AKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACG
GLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQ
QTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFF
PNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCN
VWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 5 (G), FASTA

>9K07_5 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
ASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPF
REKKFFCAIL

Sequence of entity 6 (N), FASTA

>9K07_6 Nanobody-35 (chains N)
MAQVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVRQAPGKGLEWVSDISQSGASI
SYTGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCARCPAPFTRDCFDVTSTTYAYR
GQGTQVTVSSHHHHHHEPEA

Ligands and cofactors

ID	Name	Formula	Copies
A1EL6	[(1~{S})-1-[1,4-dimethoxy-8-nitroso-5-(oxidanylamino)naphthalen-2-yl]-2,2-dimet…	C23 H24 N2 O7	1

Primary citation

Divergent activation patterns of BRS3 revealed by two Chinese herb-derived agonists. Li, J., Li, C., Zhou, Q. et al. Acta Pharm Sin B (2025) 15:5231-5243. DOI 10.1016/j.apsb.2025.06.025 · PubMed

Other PDB entries of the same protein (UniProt P32247 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8Y52 2.9 Å, Cryo-EM structure of the BA1-bound BRS3-Gq complex
9M0J 2.9 Å, Cryo-EM structure of Bombesin receptor type-3 bound to oridonin
8Y53 2.93 Å, Cryo-EM structure of the MK-5046-bound BRS3-Gq complex
9LWP 2.93 Å, Cryo-EM structure of the unliganded human BRS3-Gq complex
8Y51 3.3 Å, Cryo-EM structure of the BRS3-Gq complex

Browse structure collections

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