8JGG: Gi-coupled MRGPRX1 with peptide agonist BAM8-22

CryoEM structure of Gi-coupled MRGPRX1 with peptide agonist BAM8-22. Determined by electron microscopy at 3.0 Å resolution. Released 10 Jan 2024.

Method: Electron microscopy
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 6
Atoms: 7,889
Mol. weight: 153.85 kDa
Released: 10 Jan 2024

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

Secondary structure: helices and β-sheets

8JGG contains 37 α-helices and 58 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: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	10-18	9
α-helix	21-30	10
β-strand	34-39	6	7
α-helix	46-52	7
β-strand	185-190	6	7
β-strand	195-200	6	7
α-helix	208-210	3
β-strand	220-224	5	7
α-helix	242-254	13
β-strand	263-267	5	7
α-helix	272-280	9
α-helix	283-285	3
α-helix	296-308	13
β-strand	319-322	4	7
α-helix	331-350	20

Chain B: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	10-24	15
α-helix	30-34	5
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
α-helix	95	1
β-strand	100-105	6	10
β-strand	111-116	6	10
β-strand	121-125	5	10
α-helix	129-131	3
β-strand	134-139	6	10
β-strand	146-153	8	11
β-strand	156-161	6	11
β-strand	165-170	6	11
β-strand	176-180	5	11
β-strand	187-192	6	12
β-strand	199-203	5	12
β-strand	207-210	4	12
β-strand	220-223	4	12
β-strand	229-234	6	13
β-strand	241-245	5	13
β-strand	250-254	5	13
β-strand	259-264	6	13
β-strand	273-278	6	14
β-strand	284-289	6	14
β-strand	294-298	5	14
β-strand	304-308	5	14
β-strand	315-320	6	8
β-strand	327-331	5	8
β-strand	336-339	4	8

Chain G: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	10-23	14
α-helix	30-43	14
α-helix	45-47	3
α-helix	54-55	2
α-helix	60-63	4

Chain L: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	16-18	3

Chain R: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	30-32	3
α-helix	36-51	16
α-helix	62-83	22
α-helix	99-125	27
α-helix	127-132	6
α-helix	138-158	21
α-helix	176-202	27
α-helix	213-223	11
α-helix	230-235	6
α-helix	248-250	3
α-helix	255-269	15
α-helix	270-274	5

Chain S: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11	1	2
β-strand	17-25	9	1
α-helix	29-31	3
β-strand	33-39	7	3
β-strand	45-51	7	3
α-helix	53-55	3
β-strand	58-60	3	3
α-helix	62-64	3
β-strand	68-73	6	1
β-strand	78-84	7	1
β-strand	93-99	7	3
β-strand	111	1	3
β-strand	115-116	2	3
β-strand	118	1	2
α-helix	126-127	2
β-strand	128-129	2	4
β-strand	134-136	3	5
β-strand	143-149	7	4
β-strand	154	1	6
β-strand	160	1	6
β-strand	162-167	6	5
β-strand	174-178	5	5
β-strand	182-183	2	5
α-helix	184	1
β-strand	191-195	5	4
β-strand	199-204	6	4
β-strand	214-219	6	5
β-strand	231-234	4	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	60	Homo sapiens	P59768 (AlphaFold model)
BAM8-22	L	protein	11	Homo sapiens	P01210 (AlphaFold model)
Single-Chain Fragment Variable 16	S	protein	285	Homo sapiens
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	354	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	352	Homo sapiens	P62873 (AlphaFold model)
Mas-related G-protein coupled receptor member X1	R	protein	322	Homo sapiens	Q96LB2

Sequence of entity 1 (G), FASTA

>8JGG_1 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
NTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFREK

Sequence of entity 2 (L), FASTA

>8JGG_2 BAM8-22 (chains L)
PEWWMDYQKRY

Sequence of entity 3 (S), FASTA

>8JGG_3 Single-Chain Fragment Variable 16 (chains S)
MLLVNQSHQGFNKEHTSKMVSAIVLYVLLAAAAHSAFAVQLVESGGGLVQPGGSRKLSCS
ASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYADTVKGRFTISRDDPKNTLFLQM
TSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSAGGGGSGGGGSGGGGSADIVMTQ
ATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDR
FSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFGAGTKLEL

Sequence of entity 4 (A), FASTA

>8JGG_4 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 5 (B), FASTA

>8JGG_5 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
LEVLFQGPCGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTR
RTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPS
GNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCAL
WDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESD
INAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAG
YDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 6 (R), FASTA

>8JGG_6 Mas-related G-protein coupled receptor member X1 (chains R)
MDPTISTLDTELTPINGTEETLCYKQTLSLTVLTCIVSLVGLTGNAVVLWLLGCRMRRNA
FSIYILNLAAADFLFLSGRLIYSLLSFISIPHTISKILYPVMMFSYFAGLSFLSAVSTER
CLSVLWPIWYRCHRPTHLSAVVCVLLWALSLLRSILEWMLCGFLFSGADSAWCQTSDFIT
VAWLIFLCVVLCGSSLVLLIRILCGSRKIPLTRLYVTILLTVLVFLLCGLPFGIQFFLFL
WIHVDREVLFCHVHLVSIFLSALNSSANPIIYFFVGSFRQRQNRQNLKLVLQRALQDASE
VDEGGGQLPEEILELSGSRLEQ

Primary citation

Ligand recognition and G protein coupling of the human itch receptor MRGPRX1. Guo, L., Zhang, Y., Fang, G. et al. Nat Commun (2023) 14:5004-5004. DOI 10.1038/s41467-023-40705-z · PubMed

Other PDB entries of the same protein (UniProt P59768 (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…
7MBX 1.95 Å, Human Cholecystokinin 1 receptor (CCK1R) Gs complex
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
9EJZ 2.06 Å, Human M5 muscarinic acetylcholine receptor complex with mini-Gq, agonist acetylcholine…
6X18 2.1 Å, GLP-1 peptide hormone bound to Glucagon-Like peptide-1 (GLP-1) Receptor

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