7VDH: Mas-related G-protein coupled receptor member X2

Cryo-EM structure of pseudoallergen receptor MRGPRX2 complex with C48/80, state2. Determined by electron microscopy at 2.9 Å resolution. Released 1 Dec 2021.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 5
Atoms: 8,710
Mol. weight: 154.6 kDa
Ligands: CLR, 6IB
Released: 1 Dec 2021

Explore 7VDH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7VDH contains 39 α-helices and 59 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: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-31	25
β-strand	34-38	5	1
α-helix	46-53	8
β-strand	185-190	6	1
β-strand	195-200	6	1
α-helix	208-211	4
α-helix	212-215	4
β-strand	220-226	7	1
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	319-323	5	1
α-helix	331-350	20

Chain B: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	3-23	21
α-helix	30-33	4
α-helix	38-39	2
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	121-125	5	4
β-strand	134-139	6	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	199-203	5	6
β-strand	207-210	4	6
β-strand	220-223	4	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
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 G: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	8-23	16
α-helix	27-29	3
α-helix	30-43	14
α-helix	45-47	3
α-helix	53-55	3

Chain R: 18 helices, 0 β-strands

Element	Residues	Length
α-helix	28-30	3
α-helix	31-53	23
α-helix	54-58	5
α-helix	60-61	2
α-helix	63-90	28
α-helix	91-95	5
α-helix	104-132	29
α-helix	134-135	2
α-helix	136-140	5
α-helix	145-166	22
α-helix	177-212	36
α-helix	218-231	14
α-helix	232-236	5
α-helix	237-244	8
α-helix	246-249	4
α-helix	257-276	20
α-helix	277-282	6
α-helix	283-284	2

Chain S: 4 helices, 25 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
α-helix	53-55	3
β-strand	58-60	3	10
β-strand	65	1	9
β-strand	68-73	6	9
β-strand	78-84	7	9
β-strand	92-99	8	10
β-strand	110-111	2	10
β-strand	115-119	5	10
β-strand	128-129	2	11
β-strand	134-136	3	12
β-strand	143-149	7	11
β-strand	154	1	13
β-strand	160	1	13
β-strand	162-167	6	12
β-strand	173-178	6	12
β-strand	182-183	2	12
α-helix	184	1
β-strand	191-196	6	11
β-strand	199-204	6	11
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 X2	R	protein	330	Homo sapiens	Q96LB1 (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	G	protein	58	Homo sapiens	P59768 (AlphaFold model)
scFv	S	protein	285	Homo sapiens

Sequence of entity 1 (R), FASTA

>7VDH_1 Mas-related G-protein coupled receptor member X2 (chains R)
MDPTTPAWGTESTTVNGNDQALLLLCGKETLIPVFLILFIALVGLVGNGFVLWLLGFRMR
RNAFSVYVLSLAGADFLFLCFQIINCLVYLSNFFCSISINFPSFFTTVMTCAYLAGLSML
STVSTERCLSVLWPIWYRCRRPRHLSAVVCVLLWALSLLLSILEGKFCGFLFSDGDSGWC
QTFDFITAAWLIFLFMVLCGSSLALLVRILCGSRGLPLTRLYLTILLTVLVFLLCGLPFG
IQWFLILWIWKDSDVLFCHIHPVSVVLSSLNSSANPIIYFFVGSFRKQWRLQQPILKLAL
QRALQDIAEVDHSEGCFRQGTPEMSRSSLV

Sequence of entity 2 (A), FASTA

>7VDH_2 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 3 (B), FASTA

>7VDH_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 (G), FASTA

>7VDH_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
NTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFR

Sequence of entity 5 (S), FASTA

>7VDH_5 scFv (chains S)
MLLVNQSHQGFNKEHTSKMVSAIVLYVLLAAAAHSAFAVQLVESGGGLVQPGGSRKLSCS
ASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYADTVKGRFTISRDDPKNTLFLQM
TSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSAGGGGSGGGGSGGGGSADIVMTQ
ATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDR
FSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFGAGTKLEL

Ligands and cofactors

ID	Name	Formula	Copies
CLR	Cholesterol	C27 H46 O	1
6IB	2-[4-methoxy-3-[[2-methoxy-3-[[2-methoxy-5-[2-(methylamino)ethyl]phenyl]methyl]…	C32 H45 N3 O3	1

Primary citation

Structure, function and pharmacology of human itch receptor complexes. Yang, F., Guo, L., Li, Y. et al. Nature (2021) 600:164-169. DOI 10.1038/s41586-021-04077-y · PubMed

Other PDB entries of the same protein (UniProt Q96LB1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7S8L 2.45 Å, CryoEM structure of Gq-coupled MRGPRX2 with peptide agonist Cortistatin-14
7S8M 2.54 Å, CryoEM structure of Gi-coupled MRGPRX2 with peptide agonist Cortistatin-14
7S8O 2.58 Å, CryoEM structure of Gi-coupled MRGPRX2 with small molecule agonist (R)-Zinc-3573
7VV5 2.76 Å, Cryo-EM structure of pseudoallergen receptor MRGPRX2 complex with C48/80, state1
9WVX 2.8 Å, CryoEM structure of MRGPRX2 with peptide agonist DKD2
7VUY 2.84 Å, Cryo-EM structure of pseudoallergen receptor MRGPRX2 complex with PAMP-12. state1
7VUZ 2.89 Å, Cryo-EM structure of pseudoallergen receptor MRGPRX2 complex with PAMP-12, state2
7S8N 2.9 Å, CryoEM structure of Gq-coupled MRGPRX2 with small molecule agonist (R)-Zinc-3573
7VV3 2.97 Å, Cryo-EM structure of pseudoallergen receptor MRGPRX2 complex with linear cortistatin-14
7VV4 2.97 Å, Cryo-EM structure of pseudoallergen receptor MRGPRX2 complex with linear cortistatin-14,…
7VDM 2.98 Å, Cryo-EM structure of pseudoallergen receptor MRGPRX2 complex with substance P
7VDL 3.22 Å, Cryo-EM structure of pseudoallergen receptor MRGPRX2 complex with circular cortistatin-14

Browse structure collections

About this viewer

MolViewer shows 7VDH 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.