8DWH: Gq-coupled MRGPRX1 with ligand Compound-16

CryoEM structure of Gq-coupled MRGPRX1 with ligand Compound-16. Determined by electron microscopy at 3.25 Å resolution. Released 2 Nov 2022.

Method: Electron microscopy
Resolution: 3.25 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,444
Mol. weight: 110.41 kDa
Ligands: U2U
Released: 2 Nov 2022

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

Secondary structure: helices and β-sheets

8DWH contains 27 α-helices and 37 β-strands across 4 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: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	7-31	25
β-strand	33-35	3	1
β-strand	38-40	3	2
β-strand	69	1	3
β-strand	72-76	5	1
β-strand	79-83	5	1
β-strand	86	1	3
α-helix	96-101	6
β-strand	105-111	7	2
α-helix	118-130	13
α-helix	132-134	3
β-strand	138-144	7	2
α-helix	146-155	10
α-helix	160-162	3
α-helix	165-169	5
α-helix	184-203	20
β-strand	211-215	5	2
α-helix	223-242	20

Chain C: 2 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-22	19
α-helix	30-33	4
β-strand	47-51	5	4
β-strand	58-63	6	5
β-strand	69-74	6	5
β-strand	78-83	6	5
β-strand	89-94	6	5
β-strand	100-105	6	6
β-strand	111-116	6	6
β-strand	121-125	5	6
β-strand	135-139	5	6
β-strand	146-151	6	7
β-strand	156-161	6	7
β-strand	166-170	5	7
β-strand	175-180	6	7
β-strand	187-192	6	8
β-strand	198-203	6	8
β-strand	208-212	5	8
β-strand	218-222	5	8
β-strand	229-234	6	9
β-strand	240-245	6	9
β-strand	250-254	5	9
β-strand	260-264	5	9
β-strand	273-278	6	10
β-strand	284-289	6	10
β-strand	294-298	5	10
β-strand	306-308	3	10
β-strand	315-320	6	4
β-strand	327-331	5	4
β-strand	335-339	5	4

Chain D: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	12-23	12
α-helix	30-43	14

Chain R: 14 helices, 0 β-strands

Element	Residues	Length
α-helix	26-54	29
α-helix	60-87	28
α-helix	95-125	31
α-helix	127-128	2
α-helix	129-133	5
α-helix	138-160	23
α-helix	173-203	31
α-helix	212-224	13
α-helix	225-229	5
α-helix	231-234	4
α-helix	238-241	4
α-helix	246-251	6
α-helix	255-272	18
α-helix	274-277	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Gs-mini-Gq chimera	B	protein	246	Homo sapiens
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	C	protein	345	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)
Mas-related G-protein coupled receptor member X1	R	protein	323	Homo sapiens	Q96LB2 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>8DWH_1 Gs-mini-Gq chimera (chains B)
MGSTVSAEDKAAAERSKMIDKNLREDGEKARRTLRLLLLGADNSGKSTIVKQMRILHGGS
GGSGGTSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQE
ALNDFKSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEP
GEDPRVTRAKYFIRKEFVDISTASGDGRHICYPHFTCAVDTENARRIFNDCKDIILQMNL
REYNLV

Sequence of entity 2 (C), FASTA

>8DWH_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains C)
GPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHL
AKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACG
GLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQ
QTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFF
PNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCN
VWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (D), FASTA

>8DWH_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains D)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (R), FASTA

>8DWH_4 Mas-related G-protein coupled receptor member X1 (chains R)
GPDPTISTLDTELTPINGTEETLCYKQTLSLTVLTCIVSLVGLTGNAVVLWLLGCRMRRN
AFSIYILNLAAADFLFLSGRLIYSLLSFISIPHTISKILYPVMMFSYFAGLSFLSAVSTE
RCLSVLWPIWYRCHRPTHLSAVVCVLLWALSLLRSILEWMLCGFLFSGADSAWCQTSDFI
TVAWLIFLCVVLCGSSLVLLIRILCGSRKIPLTRLYVTILLTVLVFLLCGLPFGIQFFLF
LWIHVDREVLFCHVHLVSIFLSALNSSANPIIYFFVGSFRQRQNRQNLKLVLQRALQDAS
EVDEGGGQLPEEILELSGSRLEQ

Ligands and cofactors

ID	Name	Formula	Copies
U2U	N-{2-[(1-aminoisoquinolin-6-yl)oxy]-4-methylphenyl}-2-methoxybenzene-1-sulfonam…	C23 H21 N3 O4 S	1

Primary citation

Ligand recognition and allosteric modulation of the human MRGPRX1 receptor. Liu, Y., Cao, C., Huang, X.P. et al. Nat Chem Biol (2023) 19:416-422. DOI 10.1038/s41589-022-01173-6 · 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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