› 7evy

Electron Microscopy
2.98Å resolution

Cryo-EM structure of siponimod -bound Sphingosine-1-phosphate receptor 1 in complex with Gi protein

Released:
DOI: 10.2210/pdb7evy/pdb
PDB entry 7evy coloured by chain, front view.
PDB entry 7evy coloured by chain, side view.
PDB entry 7evy coloured by chain, top view.
Source organisms:
Primary publication:
Structures of signaling complexes of lipid receptors S1PR1 and S1PR5 reveal mechanisms of activation and drug recognition.
Yuan Y, Jia G, Wu C, Wang W, Cheng L, Li Q, Li Z, Luo K, Yang S, Yan W, Su Z, Shao Z
OpenAccess logo Cell Res 31 1263-1274 (2021)
PMID: 34526663
Related structures: EMD-31341

Function and Biology Details

Reaction catalysed: 
Hydrolysis of (1->4)-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrins
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
PDBe Complex ID:
PDB-CPX-207767 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 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: 356 amino acids
Theoretical weight: 39.14 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: C
Molecule details ›
Chain: C
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
Endolysin; Sphingosine 1-phosphate receptor 1 Chain: D
Molecule details ›
Chain: D
Length: 531 amino acids
Theoretical weight: 60.27 KDa
Source organisms: Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: D9IEF7 (Residues: 2-161; Coverage: 98%)
  • Canonical: P21453 (Residues: 1-337; Coverage: 88%)
Gene names: CHEDG1, EDG1, S1PR1, T4Tp126, e
Sequence domains:
scFv16 Chain: E
Molecule details ›
Chain: E
Length: 266 amino acids
Theoretical weight: 28.64 KDa
Source organism: Mus musculus
Expression system: Spodoptera frugiperda

Ligands and Environments

2 bound ligands:
Ligand J8C 1 x J8C
Ligand NAG 1 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.98Å
Relevant EMDB volumes: EMD-31341
Expression system: Spodoptera frugiperda

Quick links

Citations

5 review citations

Current advancements and future perspectives of long noncoding RNAs in lipid metabolism and signaling.
Duan et al. (2023)
4 more

2 mentions without citation

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