8YRG: Fospropofol-bound MRGPRX4-Gq complex

CryoEM structure of fospropofol-bound MRGPRX4-Gq complex. Determined by electron microscopy at 3.14 Å resolution. Released 22 May 2024.

Method: Electron microscopy
Resolution: 3.14 Å
Organisms: Homo sapiens, Mus musculus
Chains: 5
Atoms: 7,977
Mol. weight: 157.72 kDa
Ligands: A1LZU
Released: 22 May 2024

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

Secondary structure: helices and β-sheets

8YRG contains 33 α-helices and 60 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 B: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-30	24
β-strand	33-39	7	1
β-strand	69-76	8	1
β-strand	79-86	8	1
α-helix	96-101	6
β-strand	105-111	7	1
α-helix	118-129	12
α-helix	132-134	3
β-strand	138-144	7	1
α-helix	146-155	10
α-helix	160-163	4
α-helix	165-167	3
α-helix	184-201	18
β-strand	211-215	5	1
α-helix	224-242	19

Chain C: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-24	21
α-helix	30-34	5
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	89-94	6	3
α-helix	95	1
β-strand	100-105	6	4
β-strand	111-116	6	4
β-strand	121-125	5	4
β-strand	134-139	6	4
β-strand	146-153	8	5
β-strand	156-161	6	5
β-strand	165-169	5	5
β-strand	176-180	5	5
β-strand	187-192	6	6
β-strand	198-203	6	6
β-strand	207-212	6	6
β-strand	218-222	5	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	304-308	5	8
β-strand	315-320	6	2
β-strand	327-331	5	2
β-strand	335-339	5	2

Chain D: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	13-23	11
α-helix	30-42	13
α-helix	53-55	3

Chain E: 5 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	11-12	2	10
β-strand	19-25	7	9
α-helix	29-31	3
β-strand	33-39	7	11
β-strand	45-51	7	11
α-helix	53-55	3
β-strand	58-60	3	11
β-strand	68-73	6	9
β-strand	78-83	6	9
α-helix	88-90	3
β-strand	92-99	8	11
β-strand	111-117	7	11
β-strand	118-119	2	10
β-strand	129	1	12
β-strand	134-135	2	13
β-strand	141	1	14
β-strand	144-147	4	15
β-strand	148	1	12
β-strand	154	1	16
β-strand	160	1	16
β-strand	162-167	6	13
β-strand	174-178	5	13
β-strand	182-183	2	13
α-helix	184	1
β-strand	191-196	6	15
β-strand	199-204	6	15
β-strand	207	1	14
β-strand	214-219	6	13
α-helix	225	1
β-strand	232-233	2	13

Chain R: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	28-50	23
α-helix	51-55	5
α-helix	62-87	26
α-helix	92-125	34
α-helix	127-132	6
α-helix	138-152	15
α-helix	179-203	25
α-helix	211-227	17
α-helix	230-241	12
α-helix	246-249	4
α-helix	250-254	5
α-helix	255-273	19

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	358	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)
scFv16	E	protein	267	Mus musculus
Soluble cytochrome b562,Mas-related G-protein coupled receptor member X4	R	protein	472	Homo sapiens	P0ABE7 (AlphaFold model), Q96LA9 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>8YRG_1 Gs-mini-Gq chimera (chains B)
MGSTVSAEDKAAAERSKMIDKNLREDGEKARRTLRLLLLGADNSGKSTIVKQMRILHGGS
GGSGGTSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQE
ALNDFKSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEP
GEDPRVTRAKYFIRKEFVDISTASGDGRHICYPHFTCAVDTENARRIFNDCKDIILQMNL
REYNLV

Sequence of entity 2 (C), FASTA

>8YRG_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains C)
MHHHHHHLEVLFQGPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGR
IQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMT
CAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSG
DTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTF
TGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSG
RLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (D), FASTA

>8YRG_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains D)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (E), FASTA

>8YRG_4 scFv16 (chains E)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAALEVLFQGPHHHHHHHH

Sequence of entity 5 (R), FASTA

>8YRG_5 Soluble cytochrome b562,Mas-related G-protein coupled receptor member X4 (chains R)
DYKDDDDAKLQTMHHHHHHHHHHENLYFQGGTTMADLEDNWETLNDNLKVIEKADNAAQV
KDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKE
AQAAAEQLKTTRNAYIQKYLGSTLEVLFQGPDPTVPVFGTKLTPINGREETPCYNQTLSF
TVLTCIISLVGLTGNAVVLWLLGYRMRRNAVSIYILNLAAADFLFLSFQIIRSPLRLINI
SHLIRKILVSVMTFPYFTGLSMLSAISTERCLSVLWPIWYRCRRPTHLSAVVCVLLWGLS
LLFSMLEWRFCDFLFSGADSSWCETSDFIPVAWLIFLCVVLCVSSLVLLVRILCGSRKMP
LTRLYVTILLTVLVFLLCGLPFGILGALIYRMHLNLEVLYCHVYLVCMSLSSLNSSANPI
IYFFVGSFRQRQNRQNLKLVLQRALQDKPEVDKGEGQLPEESLELSGSRLGP

Ligands and cofactors

ID	Name	Formula	Copies
A1LZU	[2,6-di(propan-2-yl)phenoxy]methyl dihydrogen phosphate	C13 H21 O5 P	1

Primary citation

MRGPRX4 mediates phospho-drug-associated pruritus in a humanized mouse model. Chien, D.C., Limjunyawong, N., Cao, C. et al. Sci Transl Med (2024) 16:eadk8198-eadk8198. DOI 10.1126/scitranslmed.adk8198 · 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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