8JGB: Gi-coupled MRGPRX1 with peptide agonist CNF-Tx2

CryoEM structure of Gi-coupled MRGPRX1 with peptide agonist CNF-Tx2. Determined by electron microscopy at 2.84 Å resolution. Released 10 Jan 2024.

Method: Electron microscopy
Resolution: 2.84 Å
Organisms: Conus textile, Homo sapiens
Chains: 6
Atoms: 7,796
Mol. weight: 154.82 kDa
Released: 10 Jan 2024

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

Secondary structure: helices and β-sheets

8JGB contains 37 α-helices and 59 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: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-30	24
β-strand	34-40	7	1
α-helix	46-52	7
β-strand	185-190	6	1
β-strand	195-200	6	1
α-helix	208-210	3
α-helix	212-215	4
β-strand	220-226	7	1
α-helix	242-254	13
β-strand	263-269	7	1
α-helix	275-278	4
α-helix	283-285	3
α-helix	296-308	13
β-strand	319-323	5	1
α-helix	331-350	20

Chain B: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	8-19	12
α-helix	30-34	5
α-helix	37-39	3
β-strand	47-52	6	2
β-strand	58-63	6	3
β-strand	69-74	6	3
β-strand	78-83	6	3
β-strand	88-94	7	3
β-strand	100-105	6	4
β-strand	111-116	6	4
β-strand	120-125	6	4
β-strand	134-140	7	4
β-strand	146-153	8	5
β-strand	156-161	6	5
β-strand	165-170	6	5
β-strand	175-180	6	5
β-strand	187-192	6	6
β-strand	198-203	6	6
β-strand	207-212	6	6
β-strand	218-223	6	6
β-strand	229-234	6	7
β-strand	240-245	6	7
β-strand	250-254	5	7
β-strand	259-264	6	7
α-helix	272	1
β-strand	273-278	6	8
β-strand	284-289	6	8
β-strand	294-298	5	8
β-strand	303-308	6	8
β-strand	315-320	6	2
β-strand	327-331	5	2
β-strand	335-339	5	2

Chain G: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	11-21	11
α-helix	30-44	15
α-helix	45-47	3
α-helix	53-55	3
α-helix	56-58	3

Chain R: 18 helices, 0 β-strands

Element	Residues	Length
α-helix	32-35	4
α-helix	38-54	17
α-helix	60-80	21
α-helix	81-83	3
α-helix	98-125	28
α-helix	127-128	2
α-helix	129-133	5
α-helix	135	1
α-helix	138-159	22
α-helix	177-195	19
α-helix	197-200	4
α-helix	212-227	16
α-helix	230-232	3
α-helix	233-236	4
α-helix	237-239	3
α-helix	252-264	13
α-helix	269	1
α-helix	270-274	5

Chain S: 1 helix, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	11-12	2	10
β-strand	17-25	9	9
α-helix	29-31	3
β-strand	33-39	7	11
β-strand	45-51	7	11
β-strand	58-60	3	11
β-strand	68-73	6	9
β-strand	78-84	7	9
β-strand	92-99	8	11
β-strand	110-111	2	11
β-strand	115-117	3	11
β-strand	118-119	2	10
β-strand	139-141	3	12
β-strand	145-147	3	13
β-strand	154-160	7	12
β-strand	165	1	14
β-strand	171	1	14
β-strand	173-178	6	13
β-strand	185-189	5	13
β-strand	193-194	2	13
β-strand	202-207	6	12
β-strand	210-215	6	12
β-strand	224-230	7	13
β-strand	237-238	2	13
β-strand	242-245	4	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Conorfamide-Tx2	L	protein	18	Conus textile	P0DM27 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	60	Homo sapiens	P59768 (AlphaFold model)
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	358	Homo sapiens	P62873 (AlphaFold model)
Mas-related G-protein coupled receptor member X1	R	protein	319	Homo sapiens	Q96LB2
scFv16	S	protein	285	Homo sapiens

Sequence of entity 1 (L), FASTA

>8JGB_1 Conorfamide-Tx2 (chains L)
HSGILLAWSGPRNRFVRI

Sequence of entity 2 (G), FASTA

>8JGB_2 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
NTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFREK

Sequence of entity 3 (A), FASTA

>8JGB_3 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 4 (B), FASTA

>8JGB_4 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHLEVLFQGPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGR
IQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMT
CAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSG
DTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTF
TGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSG
RLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 5 (R), FASTA

>8JGB_5 Mas-related G-protein coupled receptor member X1 (chains R)
MDPTISTLDTELTPINGTEETLCYKQTLSLTVLTCIVSLVGLTGNAVVLWLLGCRMRRNA
FSIYILNLAAADFLFLSGRLIYSLLSFISIPHTISKILYPVMMFSYFAGLSFLSAVSTER
CLSVLWPIWYRCHRPTHLSAVVCVLLWALSLLRSILEWMLCGFLFSGADSAWCQTSDFIT
VAWLIFLCVVLCGSSLVLLIRILCGSRKIPLTRLYVTILLTVLVFLLCGLPFGIQFFLFL
WIHVDREVLFCHVHLVSIFLSALNSSANPIIYFFVGSFRQRQNRQNLKLVLQRALQDASE
VDEGGGQLPEEILELSGSR

Sequence of entity 6 (S), FASTA

>8JGB_6 scFv16 (chains S)
MLLVNQSHQGFNKEHTSKMVSAIVLYVLLAAAAHSAFAVQLVESGGGLVQPGGSRKLSCS
ASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYADTVKGRFTISRDDPKNTLFLQM
TSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSAGGGGSGGGGSGGGGSADIVMTQ
ATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDR
FSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFGAGTKLEL

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

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