› 8kgg

Electron Microscopy
3.06Å resolution

LPS-bound P2Y10 in complex with G13

Released:
DOI: 10.2210/pdb8kgg/pdb
PDB entry 8kgg coloured by chain, front view.
PDB entry 8kgg coloured by chain, side view.
PDB entry 8kgg coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Insights into lysophosphatidylserine recognition and Gα12/13-coupling specificity of P2Y10.
Yin H, Kamakura N, Qian Y, Tatsumi M, Ikuta T, Liang J, Xu Z, Xia R, Zhang A, Guo C, Inoue A, He Y
Cell Chem Biol (2024)
PMID: 39265572
Related structures: EMD-37220

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
PDBe Complex ID:
PDB-CPX-517240 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
Guanine nucleotide-binding protein G(i) subunit alpha-2; Guanine nucleotide-binding protein subunit alpha-13 Chain: A
Molecule details ›
Chain: A
Length: 230 amino acids
Theoretical weight: 26.57 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P04899 (Residues: 1-57; Coverage: 16%)
  • Canonical: Q14344 (Residues: 203-377; Coverage: 44%)
Gene names: GNA13, GNAI2, GNAI2B
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: 345 amino acids
Theoretical weight: 37.92 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
scFv16 Chain: E
Molecule details ›
Chain: E
Length: 247 amino acids
Theoretical weight: 26.28 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 Chain: G
Molecule details ›
Chain: G
Length: 71 amino acids
Theoretical weight: 7.86 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P59768 (Residues: 1-71; Coverage: 100%)
Gene name: GNG2
Sequence domains: GGL domain
Putative P2Y purinoceptor 10 Chain: R
Molecule details ›
Chain: R
Length: 339 amino acids
Theoretical weight: 38.81 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: O00398 (Residues: 1-339; Coverage: 100%)
Gene name: P2RY10
Sequence domains: 7 transmembrane receptor (rhodopsin family)

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
Resolution: 3.06Å
Relevant EMDB volumes: EMD-37220
Expression system: Spodoptera frugiperda

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