8K4S: Gq coupled MRGPRX4 with agonist DCA-3P

CryoEM structure of Gq coupled MRGPRX4 with agonist DCA-3P. Determined by electron microscopy at 2.9 Å resolution. Released 6 Nov 2024.

Method: Electron microscopy
Resolution: 2.9 Å
Organisms: Escherichia coli, Homo sapiens, Aequorea victoria
Chains: 5
Atoms: 8,196
Mol. weight: 181.16 kDa
Ligands: JW0
Released: 6 Nov 2024

Explore 8K4S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8K4S contains 34 α-helices and 61 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: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-31	25
β-strand	33-40	8	1
β-strand	69-76	8	1
β-strand	79-86	8	1
α-helix	96-98	3
β-strand	105-110	6	1
α-helix	118-129	12
β-strand	138-143	6	1
α-helix	147-155	9
α-helix	160-163	4
α-helix	165-167	3
α-helix	184-203	20
β-strand	211-215	5	1
α-helix	224-242	19

Chain B: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-24	21
α-helix	30-34	5
β-strand	47-51	5	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	146-151	6	5
β-strand	156-161	6	5
β-strand	165-170	6	5
β-strand	176-181	6	5
β-strand	187-192	6	6
β-strand	198-203	6	6
β-strand	208-212	5	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	260-264	5	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	336-339	4	2

Chain C: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	18-21	4
α-helix	30-43	14
α-helix	53-55	3
α-helix	56-58	3

Chain D: 6 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	11-12	2	10
β-strand	18-25	8	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
β-strand	93-99	7	11
β-strand	111	1	11
α-helix	112-114	3
β-strand	115-116	2	11
β-strand	118-119	2	10
β-strand	128-129	2	12
β-strand	134-136	3	13
β-strand	142-147	6	14
β-strand	148-149	2	12
β-strand	154	1	15
β-strand	160	1	15
β-strand	162-166	5	16
β-strand	174-178	5	16
β-strand	182-183	2	16
α-helix	184	1
β-strand	192-196	5	14
β-strand	199-205	7	14
β-strand	214	1	13
β-strand	215-219	5	16
α-helix	226	1
β-strand	227	1	16
α-helix	228	1
β-strand	232-234	3	13

Chain E: 13 helices, 0 β-strands

Element	Residues	Length
α-helix	28-54	27
α-helix	62-82	21
α-helix	83-86	4
α-helix	94-125	32
α-helix	127-128	2
α-helix	129-133	5
α-helix	138-151	14
α-helix	179-203	25
α-helix	214-226	13
α-helix	230-241	12
α-helix	253-269	17
α-helix	270-274	5
α-helix	275-278	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Soluble cytochrome b562,Mas-related G-protein coupled receptor member X4,Green fluorescent protein	E	protein	710	Escherichia coli, Homo sapiens, Aequorea victoria	P0ABE7 (AlphaFold model), P42212 (AlphaFold model), Q96LA9 (AlphaFold model)
Gs-mini-Gq chimera	A	protein	246	Homo sapiens	A0A590UJY2 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	340	Homo sapiens	P62873
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	protein	80	Homo sapiens	P59768
scFv16	D	protein	254	Mus musculus

Sequence of entity 1 (E), FASTA

>8K4S_1 Soluble cytochrome b562,Mas-related G-protein coupled receptor member X4,Green fluorescent protein (chains E)
DYKDDDDKEFADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLED
KSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLMDPT
VPVFGTKLTPINGREETPCYNQTLSFTVLTCIISLVGLTGNAVVLWLLGYRMRRNAVSIY
ILNLAAADFLFLSFQIIRLPLRLINISHLIRKILVSVMTFPYFTGLSMLSAISTERCLSV
LWPIWYRCRRPTHLSAVVCVLLWGLSLLFSMLEWRFCDFLFSGADSSWCETSDFIPVAWL
IFLCVVLCVSSLVLLVRILCGSRKMPLTRLYVTILLTVLVFLLCGLPFGILGALIYRMHL
NLEVLYCHVYLVCMSLSSLNSSANPIIYFFVGSFRQRQNRQNLKLVLQRALQDKPEVDKG
EGQLPEESLELSGSRLGPLELEVLFQGPSKGEELFTGVVPILVELDGDVNGHKFSVRGEG
EGDATNGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKRHDFFKSAMPEGYV
QERTISFKDDGTYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNFNSHNVYIT
ADKQKNGIKANFKIRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSVLSKDPNE
KRDHMVLLEFVTAAGITHGMDEWSHPQFEKGGGSGGGSGGSAWSHPQFEK

Sequence of entity 2 (A), FASTA

>8K4S_2 Gs-mini-Gq chimera (chains A)
MGSTVSAEDKAAAERSKMIDKNLREDGEKARRTLRLLLLGADNSGKSTIVKQMRILHGGS
GGSGGTSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQE
ALNDFKSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEP
GEDPRVTRAKYFIRKEFVDISTASGDGRHICYPHFTCAVDTENARRIFNDCKDIILQMNL
REYNLV

Sequence of entity 3 (B), FASTA

>8K4S_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
GSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYA
MHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNI
CSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTF
TGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNA
FATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDAL
KADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 4 (C), FASTA

>8K4S_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAILGSAGSAGSA

Sequence of entity 5 (D), FASTA

>8K4S_5 scFv16 (chains D)
GSMDVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGT
IYYADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTL
TVSSGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWF
LQRPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPL
TFGAGTKLELKAAA

Ligands and cofactors

ID	Name	Formula	Copies
JW0	(4~{R})-4-[(3~{R},5~{R},8~{R},9~{S},10~{S},12~{S},13~{R},14~{S},17~{R})-10,13-d…	C24 H41 O7 P	1

Primary citation

Structure-guided discovery of bile acid derivatives for treating liver diseases without causing itch. Yang, J., Zhao, T., Fan, J. et al. Cell (2024) 187:7164-7182.e18. DOI 10.1016/j.cell.2024.10.001 · PubMed

Other PDB entries of the same protein (UniProt P0ABE7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6DYF 1.1 Å, Cu(II)-bound structure of the engineered cyt cb562 variant, CH3Y
5YO6 1.2 Å, Crystal Structure of B562RIL with engineered disulfide bond T9C-A36C
4JEA 1.22 Å, Crystal structure of an engineered Zn-RIDC1 construct with four interfacial disulfide…
7LSJ 1.26 Å, Cu-bound crystal structure of the engineered cyt cb562 variant, DiCyt2 - H63A,…
7MK4 1.27 Å, Co-bound crystal structure of the engineered cyt cb562 variant, DiCyt2
6DYC 1.33 Å, Co(II)-bound structure of the engineered cyt cb562 variant, CH3
5YO4 1.37 Å, Crystal Structure of B562RIL with engineered disulfide bond K27C-A79C
256B 1.4 Å, Improvement of the 2.5 Å resolution model of cytochrome B562 by redetermining the…
6OT4 1.4 Å, Bimetallic dodecameric cage design 2 (BMC2) from cytochrome cb562
7LRV 1.4 Å, Ni-bound crystal structure of the engineered cyt cb562 variant, DiCyt2, crystallized in…
9PQ4 1.48 Å, Bi-bound structure of the H77C variant of TriCyt2
6DYG 1.49 Å, Fe(II)-bound structure of the engineered cyt cb562 variant, CH3Y

Browse structure collections

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