8Y53: MK-5046-bound BRS3-Gq complex

Cryo-EM structure of the MK-5046-bound BRS3-Gq complex. Determined by electron microscopy at 2.93 Å resolution. Released 11 Sept 2024.

Method: Electron microscopy
Resolution: 2.93 Å
Organisms: Homo sapiens, Mus musculus, Lama glama
Chains: 6
Atoms: 10,071
Mol. weight: 170.84 kDa
Ligands: A1D54
Released: 11 Sept 2024

Explore 8Y53 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Y53 contains 37 α-helices and 73 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: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-32	26
β-strand	34-39	6	1
α-helix	46-52	7
β-strand	185-191	7	1
β-strand	194-200	7	1
α-helix	211-215	5
β-strand	220-226	7	1
α-helix	230-244	15
β-strand	254-259	6	1
α-helix	261-270	10
α-helix	275-277	3
α-helix	280-284	5
α-helix	293-294	2
α-helix	299-317	19
β-strand	326-330	5	1
α-helix	339-357	19

Chain B: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	9-29	21
α-helix	35-38	4
α-helix	43-44	2
β-strand	52-56	5	2
β-strand	63-68	6	3
β-strand	74-79	6	3
β-strand	83-88	6	3
β-strand	94-99	6	3
β-strand	105-110	6	4
β-strand	116-121	6	4
β-strand	126-130	5	4
β-strand	139-144	6	4
β-strand	151-156	6	5
β-strand	161-166	6	5
β-strand	171-175	5	5
β-strand	180-185	6	5
β-strand	192-197	6	6
β-strand	203-208	6	6
β-strand	213-217	5	6
β-strand	223-227	5	6
β-strand	234-239	6	7
β-strand	245-250	6	7
β-strand	254-259	6	7
β-strand	264-270	7	7
α-helix	277	1
β-strand	278-283	6	8
β-strand	289-294	6	8
β-strand	298-303	6	8
β-strand	309-313	5	8
β-strand	320-325	6	2
β-strand	332-336	5	2
β-strand	341-344	4	2

Chain E: 6 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	9
β-strand	9-11	3	10
β-strand	16-24	9	9
α-helix	28-30	3
β-strand	32-38	7	10
β-strand	44-50	7	10
α-helix	52-54	3
β-strand	57-59	3	10
β-strand	64	1	9
β-strand	67-72	6	9
β-strand	77-83	7	9
α-helix	87-89	3
β-strand	91-98	8	10
β-strand	110	1	10
β-strand	114-118	5	10
β-strand	140-142	3	11
β-strand	146	1	12
β-strand	155-161	7	11
β-strand	166	1	13
β-strand	172	1	13
β-strand	174-179	6	12
β-strand	185-189	5	12
α-helix	194	1
β-strand	195	1	12
α-helix	196	1
β-strand	203-207	5	11
β-strand	211-216	6	11
α-helix	221-223	3
β-strand	225-231	7	12
β-strand	239	1	12
β-strand	243-245	3	12

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	6-22	17
α-helix	29-43	15
α-helix	44-46	3

Chain N: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	14
β-strand	10-12	3	15
β-strand	18-25	8	14
α-helix	29-31	3
β-strand	34-39	6	16
β-strand	45-51	7	16
β-strand	58-60	3	16
β-strand	68-73	6	14
β-strand	78-83	6	14
α-helix	88-90	3
β-strand	93-98	6	16
β-strand	118	1	16
β-strand	122	1	16
β-strand	124-126	3	15

Chain R: 12 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	49-74	26
α-helix	76-78	3
α-helix	81-105	25
α-helix	118-149	32
α-helix	156-157	2
α-helix	161-184	24
β-strand	189-192	4	17
β-strand	199-202	4	17
α-helix	211-222	12
α-helix	223-227	5
α-helix	228-250	23
α-helix	260-297	38
α-helix	308-333	26
α-helix	335-344	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(q) subunit alpha	A	protein	361	Homo sapiens
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	345	Homo sapiens	P62873 (AlphaFold model)
scFv16	E	protein	247	Mus musculus
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	71	Homo sapiens	P59768 (AlphaFold model)
nanobody Nb35	N	protein	150	Lama glama
Bombesin receptor subtype-3	R	protein	361	Homo sapiens	P32247 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8Y53_1 Guanine nucleotide-binding protein G(q) subunit alpha (chains A)
MGCTLSAEDKAAVERSKMIEKQLQKDKQVYRRTLRLLLLGADNSGKSTIVKQMRIYHVNG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TSGIFETKFQVDKVNFHMFDVGAQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQEALNDF
KSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEPGEDPR
VTRAKYFIRKEFVDISTASGDGRHICYPHFTCSVDTENARRIFNDCKDIILQMNLREYNL
V

Sequence of entity 2 (B), FASTA

>8Y53_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHL
AKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACG
GLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQ
QTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFF
PNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCN
VWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (E), FASTA

>8Y53_3 scFv16 (chains E)
VQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYA
DTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSA
GGGGSGGGGSGGGGSADIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLEL

Sequence of entity 4 (G), FASTA

>8Y53_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 5 (N), FASTA

>8Y53_5 nanobody Nb35 (chains N)
MKYLLPTAAAGLLLLAAQPAMAQVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVR
QAPGKGLEWVSDISQSGASISYTGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCAR
CPAPFTRDCFDVTSTTYAYRGQGTQVTVSS

Sequence of entity 6 (R), FASTA

>8Y53_6 Bombesin receptor subtype-3 (chains R)
MAQRQPHSPNQTLISITNDTESSSSVVSNDNTNKGWSGDNSPGIEALCAIYITYAVIISV
GILGNAILIKVFFKTKSMQTVPNIFITSLAFGDLLLLLTCVPVDATHYLAEGWLFGRIGC
KVLSFIRLTSVGVSVFTLTILSADRYKAVVKPLERQPSNAILKTCVKAGCVWIVSMIFAL
PEAIFSNVYTFRDPNKNMTFESCTSYPVSKKLLQEIHSLLCFLVFYIIPLSIISVYYSLI
ARTLYKSTLNIPTEEQSHARKQIESRKRIARTVLVLVALFALCWLPNHLLYLYHSFTSQT
YVDPSAMHFIFTIFSRVLAFSNSCVNPFALYWLSKSFQKHFKAQLFCCKAERPEPPVADT
S

Ligands and cofactors

ID	Name	Formula	Copies
A1D54	(2~{S})-1,1,1-tris(fluoranyl)-2-(4-pyrazol-1-ylphenyl)-3-[5-[[1-(trifluoromethy…	C20 H18 F6 N4 O	1

Primary citation

Structural insights into ligand recognition, selectivity, and activation of bombesin receptor subtype-3. Li, C., Xu, Y., Su, W. et al. Cell Rep (2024) 43:114511-114511. DOI 10.1016/j.celrep.2024.114511 · 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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