9DQJ: Gq-coupled MRGPRD with a new agonist EP-3945

CryoEM structure of Gq-coupled MRGPRD with a new agonist EP-3945. Determined by electron microscopy at 2.9 Å resolution. Released 11 Dec 2024.

Method: Electron microscopy
Resolution: 2.9 Å
Organisms: Homo sapiens, Mus musculus
Chains: 5
Atoms: 8,043
Mol. weight: 137.67 kDa
Ligands: A1BEQ
Released: 11 Dec 2024

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

Secondary structure: helices and β-sheets

9DQJ contains 31 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 A: 12 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	141-164	24
α-helix	172-185	14
α-helix	186-190	5
α-helix	191-208	18
α-helix	217-229	13
α-helix	230-234	5
α-helix	236-246	11
α-helix	251-276	26

Chain B: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-31	25
β-strand	33-39	7	1
α-helix	46-48	3
β-strand	69-76	8	1
β-strand	79-86	8	1
α-helix	96-100	5
β-strand	105-111	7	1
α-helix	118-129	12
β-strand	138-144	7	1
α-helix	146-155	10
α-helix	160-162	3
α-helix	165-167	3
α-helix	184-204	21
β-strand	211-215	5	1
α-helix	224-242	19

Chain C: 2 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-24	21
α-helix	30-33	4
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	89-94	6	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	175-181	7	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
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	336-339	4	2

Chain D: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	13-23	11
α-helix	30-43	14
α-helix	45-47	3
α-helix	53-55	3

Chain E: 4 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	10-12	3	10
β-strand	17-25	9	9
α-helix	29-31	3
β-strand	33-39	7	10
β-strand	45-51	7	10
β-strand	58-60	3	10
β-strand	68-73	6	9
α-helix	74-76	3
β-strand	78-84	7	9
β-strand	92-99	8	10
β-strand	110-111	2	10
β-strand	113	1	9
β-strand	115-119	5	10
β-strand	129	1	11
β-strand	134-136	3	12
β-strand	143-147	5	13
β-strand	148	1	11
β-strand	154	1	14
β-strand	160	1	14
β-strand	162-167	6	12
β-strand	174-178	5	12
β-strand	182-183	2	12
α-helix	184	1
β-strand	191-196	6	13
β-strand	199-204	6	13
β-strand	214-219	6	12
α-helix	225	1
β-strand	227	1	12
β-strand	231-234	4	12

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)
Guanine nucleotide-binding protein G(i) subunit alpha-2,Guanine nucleotide-binding protein G(s)…	B	protein	246	Homo sapiens	P04899 (AlphaFold model), Q5JWF2 (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
scFv16	E	protein	257	Mus musculus

Sequence of entity 1 (A), FASTA

>9DQJ_1 Mas-related G-protein coupled receptor member D (chains A)
GPNQTLNSSGTVESALNYSRGSTVHTAYLVLSSLAMFTCLCGMAGNSMVIWLLGFRMHRN
PFCIYILNLAAADLLFLFSMASTLSLETQPLVNTTDKVHELMKRLMYFAYTVGLSLLTAI
STQRCLSVLFPIWFKCHRPRHLSAWVCGLLWTLCLLMNGLTSSFCSKFLKFNEDRCFRVD
MVQAALIMGVLTPVMTLSSLTLFVWVRRSSQQWRRQPTRLFVVVLASVLVFLICSLPLSI
YWFVLYWLSLPPEMQVLCFSLSRLSSSVSSSANPVIYFLVGSRRSHRLPTRSLGTVLQQA
LREEPELEGGETPTVGTNEMGA

Sequence of entity 2 (B), FASTA

>9DQJ_2 Guanine nucleotide-binding protein G(i) subunit alpha-2,Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas (chains B)
MGSTVSAEDKAAAERSKMIDKNLREDGEKARRTLRLLLLGADNSGKSTIVKQMRILHGGS
GGSGGTSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQE
ALNDFKSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEP
GEDPRVTRAKYFIRKEFVDISTASGDGRHICYPHFTCAVDTENARRIFNDCKDIILQMNL
REYNLV

Sequence of entity 3 (C), FASTA

>9DQJ_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

>9DQJ_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains D)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 5 (E), FASTA

>9DQJ_5 scFv16 (chains E)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAALEVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
A1BEQ	2-({1-[1-(4-methoxyphenyl)cyclopropane-1-carbonyl]piperidin-4-yl}amino)quinazol…	C24 H26 N4 O3	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
9DQH 2.92 Å, CryoEM structure of Gq-coupled MRGPRD with a new agonist EP-2825
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

About this viewer

MolViewer shows 9DQJ directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.