9WVX: MRGPRX2 with peptide agonist DKD2

CryoEM structure of MRGPRX2 with peptide agonist DKD2. Determined by electron microscopy at 2.8 Å resolution. Released 30 Sept 2026.

Method: Electron microscopy
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 6
Atoms: 8,543
Mol. weight: 155.5 kDa
Released: 30 Sept 2026

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

Secondary structure: helices and β-sheets

9WVX 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: 12 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-31	25
β-strand	34-40	7	1
α-helix	46-53	8
β-strand	185-191	7	1
β-strand	194-200	7	1
α-helix	208-210	3
α-helix	212-215	4
β-strand	220-226	7	1
α-helix	227-229	3
α-helix	232	1
β-strand	233	1	2
α-helix	234	1
β-strand	241	1	2
α-helix	242-254	13
β-strand	263-269	7	1
α-helix	271-278	8
α-helix	283-285	3
α-helix	296-308	13
β-strand	319-324	6	1
α-helix	331-350	20

Chain B: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	3-25	23
α-helix	30-33	4
α-helix	38-39	2
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	88-94	7	4
α-helix	95	1
β-strand	100-105	6	5
β-strand	111-116	6	5
β-strand	120-125	6	5
β-strand	134-140	7	5
β-strand	146-151	6	6
β-strand	156-161	6	6
β-strand	165-170	6	6
β-strand	176-181	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	250-254	5	8
β-strand	259-264	6	8
β-strand	273-278	6	9
β-strand	285-289	5	9
β-strand	294-297	4	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 C: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	8-23	16
α-helix	30-43	14
α-helix	45-47	3
α-helix	53-55	3

Chain R: 14 helices, 0 β-strands

Element	Residues	Length
α-helix	31-57	27
α-helix	65-94	30
α-helix	105-132	28
α-helix	134-139	6
α-helix	143-145	3
α-helix	146-167	22
α-helix	177-205	29
α-helix	218-228	11
α-helix	232-236	5
α-helix	240-243	4
α-helix	246-248	3
α-helix	261-266	6
α-helix	271-274	4
α-helix	275-277	3

Chain S: 3 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	11-12	2	11
β-strand	17-25	9	10
α-helix	29-31	3
β-strand	33-39	7	12
β-strand	45-51	7	12
β-strand	58-60	3	12
β-strand	65	1	10
β-strand	68-73	6	10
β-strand	78-84	7	10
α-helix	88-90	3
β-strand	92-99	8	12
β-strand	110-111	2	12
β-strand	115-117	3	12
β-strand	118-119	2	11
β-strand	129	1	13
β-strand	134-136	3	14
β-strand	143-148	6	13
β-strand	154	1	15
β-strand	160	1	15
β-strand	162-167	6	14
β-strand	174-178	5	14
β-strand	182-183	2	14
β-strand	191-196	6	13
β-strand	199-204	6	13
β-strand	214-219	6	14
α-helix	225	1
β-strand	226-227	2	14
β-strand	231-234	4	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
2-oxoadipate dehydrogenase complex component E1	L	protein	14	Homo sapiens	Q96HY7 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	354	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	358	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	protein	60	Homo sapiens	P59768 (AlphaFold model)
Mas-related G-protein coupled receptor member X2	R	protein	329	Homo sapiens	Q96LB1
scFv16	S	protein	285	Homo sapiens

Sequence of entity 1 (L), FASTA

>9WVX_1 2-oxoadipate dehydrogenase complex component E1 (chains L)
ARRGLGRALPLFWR

Sequence of entity 2 (A), FASTA

>9WVX_2 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 3 (B), FASTA

>9WVX_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHLEVLFQGPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGR
IQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMT
CAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSG
DTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTF
TGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSG
RLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 4 (C), FASTA

>9WVX_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
NTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFREK

Sequence of entity 5 (R), FASTA

>9WVX_5 Mas-related G-protein coupled receptor member X2 (chains R)
DPTTPAWGTESTTVNGNDQALLLLCGKETLIPVFLILFIALVGLVGNGFVLWLLGFRMRR
NAFSVYVLSLAGADFLFLCFQIINCLVYLSNFFCSISINFPSFFTTVMTCAYLAGLSMLS
TVSTERCLSVLWPIWYRCRRPRHLSAVVCVLLWALSLLLSILEGKFCGFLFSDGDSGWCQ
TFDFITAAWLIFLFMVLCGSSLALLVRILCGSRGLPLTRLYLTILLTVLVFLLCGLPFGI
QWFLILWIWKDSDVLFCHIHPVSVVLSSLNSSANPIIYFFVGSFRKQWRLQQPILKLALQ
RALQDIAEVDHSEGCFRQGTPEMSRSSLV

Sequence of entity 6 (S), FASTA

>9WVX_6 scFv16 (chains S)
MLLVNQSHQGFNKEHTSKMVSAIVLYVLLAAAAHSAFAVQLVESGGGLVQPGGSRKLSCS
ASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYADTVKGRFTISRDDPKNTLFLQM
TSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSAGGGGSGGGGSGGGGSADIVMTQ
ATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDR
FSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFGAGTKLEL

Primary citation

CryoEM structure of MRGPRX2 with peptide agonist DKD2. Fang, G.X. To be published.

Other PDB entries of the same protein (UniProt Q96HY7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5RW1 1.52 Å, PanDDA analysis group deposition of ground-state model of DHTKD1
5RVY 1.61 Å, PanDDA analysis group deposition -- Crystal Structure of DHTKD1 in complex with Z437516460
5RVW 1.61 Å, PanDDA analysis group deposition -- Crystal Structure of DHTKD1 in complex with…
5RVX 1.66 Å, PanDDA analysis group deposition -- Crystal Structure of DHTKD1 in complex with Z804566442
5RW0 1.67 Å, PanDDA analysis group deposition -- Crystal Structure of DHTKD1 in complex with…
6SY1 1.87 Å, Crystal structure of the human 2-oxoadipate dehydrogenase DHTKD1 (E1)
5RVZ 1.98 Å, PanDDA analysis group deposition -- Crystal Structure of DHTKD1 in complex with…
6U3J 2.25 Å, Structure of the 2-oxoadipate dehydrogenase DHTKD1

Browse structure collections

About this viewer

MolViewer shows 9WVX 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.