8JGF: Gq-coupled MRGPRX1 with peptide agonist BAM8-22

CryoEM structure of Gq-coupled MRGPRX1 with peptide agonist BAM8-22. Determined by electron microscopy at 2.7 Å resolution. Released 10 Jan 2024.

Method: Electron microscopy
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 6
Atoms: 8,338
Mol. weight: 154.9 kDa
Released: 10 Jan 2024

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

Secondary structure: helices and β-sheets

8JGF contains 39 α-helices and 58 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: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-32	26
β-strand	33-40	8	1
α-helix	46-53	8
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	233-244	12
α-helix	247-249	3
β-strand	254-259	6	1
α-helix	261-270	10
α-helix	275-277	3
α-helix	280-284	5
α-helix	299-318	20
β-strand	326-330	5	1
α-helix	338-357	20

Chain B: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	12-30	19
α-helix	35-39	5
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	93-99	7	3
α-helix	100	1
β-strand	105-110	6	4
β-strand	116-121	6	4
β-strand	125-130	6	4
β-strand	139-145	7	4
β-strand	151-158	8	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	255-259	5	7
β-strand	264-269	6	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: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	9
β-strand	9-11	3	10
β-strand	17-24	8	9
α-helix	28-30	3
β-strand	32-38	7	10
β-strand	44-50	7	10
β-strand	57-59	3	10
β-strand	67-72	6	9
β-strand	77-82	6	9
α-helix	87-89	3
β-strand	91-98	8	10
β-strand	109-110	2	10
β-strand	114-118	5	10
α-helix	138-139	2
β-strand	140-141	2	11
β-strand	146-148	3	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	186-189	4	12
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	226-231	6	12
β-strand	239	1	12
β-strand	243-246	4	12

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	10-22	13
α-helix	29-43	15
α-helix	52-54	3

Chain R: 16 helices, 0 β-strands

Element	Residues	Length
α-helix	27-29	3
α-helix	30-54	25
α-helix	61-84	24
α-helix	98-125	28
α-helix	127-128	2
α-helix	129-133	5
α-helix	138-159	22
α-helix	176-204	29
α-helix	212-224	13
α-helix	225-229	5
α-helix	230-238	9
α-helix	246-248	3
α-helix	249-254	6
α-helix	255-269	15
α-helix	270-274	5
α-helix	275-277	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein Gq	A	protein	361	Homo sapiens
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	352	Homo sapiens	P62873 (AlphaFold model)
Single-Chain Fragment Variable 16	E	protein	285	Homo sapiens
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	58	Homo sapiens	P59768 (AlphaFold model)
BAM8-22	L	protein	15	Homo sapiens	P01210 (AlphaFold model)
Mas-related G-protein coupled receptor member X1	R	protein	319	Homo sapiens	Q96LB2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8JGF_1 Guanine nucleotide-binding protein Gq (chains A)
MGCTLSAEDKAAVERSKMIEKQLQKDKQVYRRTLRLLLLGADNSGKSTIVKQMRIYHVNG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TSGIFETKFQVDKVNFHMFDVGAQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQEALNDF
KSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEPGEDPR
VTRAKYFIRKEFVDISTASGDGRHICYPHFTCSVDTENARRIFNDCKDIILQMNLREYNL
V

Sequence of entity 2 (B), FASTA

>8JGF_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
LEVLFQGPCGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTR
RTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPS
GNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCAL
WDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESD
INAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAG
YDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (E), FASTA

>8JGF_3 Single-Chain Fragment Variable 16 (chains E)
MLLVNQSHQGFNKEHTSKMVSAIVLYVLLAAAAHSAFAVQLVESGGGLVQPGGSRKLSCS
ASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYADTVKGRFTISRDDPKNTLFLQM
TSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSAGGGGSGGGGSGGGGSADIVMTQ
ATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDR
FSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFGAGTKLEL

Sequence of entity 4 (G), FASTA

>8JGF_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
NTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFR

Sequence of entity 5 (L), FASTA

>8JGF_5 BAM8-22 (chains L)
VGRPEWWMDYQKRYG

Sequence of entity 6 (R), FASTA

>8JGF_6 Mas-related G-protein coupled receptor member X1 (chains R)
MDPTISTLDTELTPINGTEETLCYKQTLSLTVLTCIVSLVGLTGNAVVLWLLGCRMRRNA
FSIYILNLAAADFLFLSGRLIYSLLSFISIPHTISKILYPVMMFSYFAGLSFLSAVSTER
CLSVLWPIWYRCHRPTHLSAVVCVLLWALSLLRSILEWMLCGFLFSGADSAWCQTSDFIT
VAWLIFLCVVLCGSSLVLLIRILCGSRKIPLTRLYVTILLTVLVFLLCGLPFGIQFFLFL
WIHVDREVLFCHVHLVSIFLSALNSSANPIIYFFVGSFRQRQNRQNLKLVLQRALQDASE
VDEGGGQLPEEILELSGSR

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 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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