› 7vdm

Electron Microscopy
2.98Å resolution

Cryo-EM structure of pseudoallergen receptor MRGPRX2 complex with substance P

Released:
DOI: 10.2210/pdb7vdm/pdb
PDB entry 7vdm coloured by chain, front view.
PDB entry 7vdm coloured by chain, side view.
PDB entry 7vdm coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure, function and pharmacology of human itch receptor complexes.
Yang F, Guo L, Li Y, Wang G, Wang J, Zhang C, Fang GX, Chen X, Liu L, Yan X, Liu Q, Qu C, Xu Y, Xiao P, Zhu Z, Li Z, Zhou J, Yu X, Gao N, Sun JP
Nature 600 164-169 (2021)
PMID: 34789875
Related structures: EMD-31923

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
PDBe Complex ID:
PDB-CPX-225523 (preferred)
Entry contents:
6 distinct polypeptide molecules
Macromolecules (6 distinct):
Guanine nucleotide-binding protein G(i) subunit alpha-1 Chain: A
Molecule details ›
Chain: A
Length: 354 amino acids
Theoretical weight: 40.42 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P63096 (Residues: 1-354; Coverage: 100%)
Gene name: GNAI1
Sequence domains: G-protein alpha subunit
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 Chain: B
Molecule details ›
Chain: B
Length: 358 amino acids
Theoretical weight: 39.42 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P62873 (Residues: 2-340; Coverage: 100%)
Gene name: GNB1
Sequence domains: WD domain, G-beta repeat
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 Chain: G
Molecule details ›
Chain: G
Length: 58 amino acids
Theoretical weight: 6.38 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P59768 (Residues: 5-62; Coverage: 82%)
Gene name: GNG2
Sequence domains: GGL domain
scFv Chain: S
Molecule details ›
Chain: S
Length: 285 amino acids
Theoretical weight: 30.36 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
Mas-related G-protein coupled receptor member X2 Chain: R
Molecule details ›
Chain: R
Length: 330 amino acids
Theoretical weight: 37.12 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q96LB1 (Residues: 1-330; Coverage: 100%)
Gene names: MRGPRX2, MRGX2
Sequence domains: 7 transmembrane receptor (rhodopsin family)
Substance P Chain: L
Molecule details ›
Chain: L
Length: 11 amino acids
Theoretical weight: 1.35 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P20366 (Residues: 58-68; Coverage: 10%)
Gene names: NKA, NKNA, TAC1, TAC2
Sequence domains: Tachykinin family

Ligands and Environments

1 bound ligand:
Ligand CLR 1 x CLR
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.98Å
Relevant EMDB volumes: EMD-31923
Expression system: Spodoptera frugiperda

Quick links

Citations

7 review citations

Specialized Pro-Resolving Mediators as Resolution Pharmacology for the Control of Pain and Itch.
Ji RR. (2023)
6 more

1 mention without citation

G protein-coupled receptors in neurodegenerative diseases and psychiatric disorders.
Wong et al. (2023)