9DQH: Gq-coupled MRGPRD with a new agonist EP-2825

CryoEM structure of Gq-coupled MRGPRD with a new agonist EP-2825. Determined by electron microscopy at 2.92 Å resolution. Released 11 Dec 2024.

Method: Electron microscopy
Resolution: 2.92 Å
Organisms: Homo sapiens, Mus musculus
Chains: 5
Atoms: 7,978
Mol. weight: 137.68 kDa
Ligands: A1BE2
Released: 11 Dec 2024

Explore 9DQH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9DQH contains 37 α-helices and 62 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: 14 helices, 0 β-strands

Element	Residues	Length
α-helix	22-51	30
α-helix	61-86	26
α-helix	92-128	37
α-helix	130-135	6
α-helix	141-162	22
α-helix	172-185	14
α-helix	186-190	5
α-helix	191-206	16
α-helix	209-211	3
α-helix	218-229	12
α-helix	230-234	5
α-helix	235-243	9
α-helix	251-273	23
α-helix	274-278	5

Chain B: 10 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	7-31	25
β-strand	33-35	3	1
β-strand	36-39	4	2
α-helix	46-48	3
β-strand	69-76	8	1
β-strand	79-86	8	1
α-helix	96-101	6
β-strand	105-111	7	2
α-helix	118-129	12
α-helix	132-134	3
β-strand	138-144	7	2
α-helix	146-155	10
α-helix	160-163	4
α-helix	165-167	3
α-helix	184-203	20
β-strand	211-215	5	2
α-helix	224-242	19

Chain C: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-25	22
α-helix	30-33	4
α-helix	34-36	3
β-strand	47-51	5	3
β-strand	58-63	6	4
β-strand	69-74	6	4
β-strand	78-83	6	4
β-strand	89-94	6	4
β-strand	100-105	6	5
β-strand	111-116	6	5
β-strand	121-125	5	5
α-helix	129-131	3
β-strand	134-139	6	5
β-strand	146-151	6	6
β-strand	156-161	6	6
β-strand	166-170	5	6
β-strand	175-180	6	6
β-strand	187-192	6	7
β-strand	198-203	6	7
β-strand	207-212	6	7
β-strand	217-223	7	7
β-strand	229-234	6	8
β-strand	240-245	6	8
β-strand	249-254	6	8
β-strand	260-264	5	8
α-helix	272	1
β-strand	273-278	6	9
β-strand	284-289	6	9
β-strand	294-298	5	9
β-strand	304-308	5	9
β-strand	315-320	6	3
β-strand	327-331	5	3
β-strand	336-339	4	3

Chain D: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	12-23	12
α-helix	30-43	14
α-helix	45-47	3
α-helix	53-55	3

Chain E: 4 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	10
β-strand	11-12	2	11
β-strand	18-25	8	10
α-helix	29-31	3
β-strand	33-39	7	12
β-strand	45-51	7	12
α-helix	53-55	3
β-strand	58-60	3	12
β-strand	68-73	6	10
β-strand	78-83	6	10
β-strand	92-99	8	12
β-strand	110-111	2	12
β-strand	113	1	10
β-strand	115-117	3	12
β-strand	118-119	2	11
α-helix	126-127	2
β-strand	128-129	2	13
β-strand	134-136	3	14
β-strand	143-147	5	15
β-strand	148-149	2	13
β-strand	154	1	16
β-strand	160	1	16
β-strand	162-167	6	14
β-strand	174-178	5	14
β-strand	182-183	2	14
β-strand	192-196	5	15
β-strand	199-204	6	15
β-strand	214-219	6	14
α-helix	225	1
β-strand	227	1	14
β-strand	231-234	4	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mas-related G-protein coupled receptor member D	A	protein	322	Homo sapiens	Q8TDS7 (AlphaFold model)
Gs-mini-Gq chimera	B	protein	246	Homo sapiens	A0A590UJY2 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	C	protein	345	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	257	Mus musculus

Sequence of entity 1 (A), FASTA

>9DQH_1 Mas-related G-protein coupled receptor member D (chains A)
GPNQTLNSSGTVESALNYSRGSTVHTAYLVLSSLAMFTCLCGMAGNSMVIWLLGFRMHRN
PFCIYILNLAAADLLFLFSMASTLSLETQPLVNTTDKVHELMKRLMYFAYTVGLSLLTAI
STQRCLSVLFPIWFKCHRPRHLSAWVCGLLWTLCLLMNGLTSSFCSKFLKFNEDRCFRVD
MVQAALIMGVLTPVMTLSSLTLFVWVRRSSQQWRRQPTRLFVVVLASVLVFLICSLPLSI
YWFVLYWLSLPPEMQVLCFSLSRLSSSVSSSANPVIYFLVGSRRSHRLPTRSLGTVLQQA
LREEPELEGGETPTVGTNEMGA

Sequence of entity 2 (B), FASTA

>9DQH_2 Gs-mini-Gq chimera (chains B)
MGSTVSAEDKAAAERSKMIDKNLREDGEKARRTLRLLLLGADNSGKSTIVKQMRILHGGS
GGSGGTSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQE
ALNDFKSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEP
GEDPRVTRAKYFIRKEFVDISTASGDGRHICYPHFTCAVDTENARRIFNDCKDIILQMNL
REYNLV

Sequence of entity 3 (C), FASTA

>9DQH_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains C)
GPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHL
AKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACG
GLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQ
QTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFF
PNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCN
VWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 4 (D), FASTA

>9DQH_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains D)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 5 (E), FASTA

>9DQH_5 scFv16 (chains E)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAALEVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
A1BE2	2-({1-[2-(4-chlorophenyl)-2-methylpropanoyl]piperidin-4-yl}amino)-5,6,7,8-tetra…	C23 H29 Cl N4 O2	1

Primary citation

High-affinity agonists reveal recognition motifs for the MRGPRD GPCR. Wang, C., Liu, Y., Lanier, M. et al. Cell Rep (2024) 43:114942-114942. DOI 10.1016/j.celrep.2024.114942 · PubMed

Other PDB entries of the same protein (UniProt Q8TDS7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7Y15 2.9 Å, Cryo-EM structure of apo-state MrgD-Gi complex
9DQJ 2.9 Å, CryoEM structure of Gq-coupled MRGPRD with a new agonist EP-3945
7Y12 3.1 Å, Cryo-EM structure of MrgD-Gi complex with beta-alanine
7Y13 3.1 Å, Cryo-EM structure of apo-state MrgD-Gi complex (local)
7Y14 3.2 Å, Cryo-EM structure of MrgD-Gi complex with beta-alanine (local)

Browse structure collections

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