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Complex structure of Neuropeptide Y Y2 receptor in complex with NPY and Gi

Electron Microscopy
3.11Å resolution
PDB entry 7yoo coloured by chain, front view.
PDB entry 7yoo coloured by chain, side view.
PDB entry 7yoo coloured by chain, top view.
Source organisms:
Assembly composition:
hetero hexamer (preferred)
Entry contents: 6 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero hexamer
Accessible surface area: 54349.8 Å2
Buried surface area: 13119.98 Å2
Dissociation area: 879.99 Å2
Dissociation energy (ΔGdiss): -5.04 kcal/mol
Dissociation entropy (TΔSdiss): 13.63 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-224952

Macromolecules

Guanine nucleotide-binding protein G(i) subunit alpha-1
Chain: A
Length: 354 amino acids
Theoretical weight: 40.42 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P63096 (Residues: 1-354; Coverage: 100%)
Gene name: GNAI1
Pfam: G-protein alpha subunit
InterPro:
Guanine nucleotide-binding protein G(i) subunit alpha-1 in PDB entry 7yoo, assembly 1, front view.
Guanine nucleotide-binding protein G(i) subunit alpha-1 in PDB entry 7yoo, assembly 1, side view.
Guanine nucleotide-binding protein G(i) subunit alpha-1 in PDB entry 7yoo, assembly 1, top view.
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Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
Chain: B
Length: 345 amino acids
Theoretical weight: 37.73 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P62873 (Residues: 2-340; Coverage: 100%)
Gene name: GNB1
Pfam: WD domain, G-beta repeat
InterPro:
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 in PDB entry 7yoo, assembly 1, front view.
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 in PDB entry 7yoo, assembly 1, side view.
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 in PDB entry 7yoo, assembly 1, top view.
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Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
Chain: G
Length: 71 amino acids
Theoretical weight: 7.86 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P59768 (Residues: 1-71; Coverage: 100%)
Gene name: GNG2
Pfam: GGL domain
InterPro:
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 in PDB entry 7yoo, assembly 1, front view.
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 in PDB entry 7yoo, assembly 1, side view.
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 in PDB entry 7yoo, assembly 1, top view.
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Neuropeptide Y
Chain: L
Length: 36 amino acids
Theoretical weight: 4.28 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P01303 (Residues: 29-64; Coverage: 52%)
Gene name: NPY
Pfam: Pancreatic hormone peptide
InterPro:
Neuropeptide Y in PDB entry 7yoo, assembly 1, front view.
Neuropeptide Y in PDB entry 7yoo, assembly 1, side view.
Neuropeptide Y in PDB entry 7yoo, assembly 1, top view.
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Neuropeptide Y receptor type 2
Chain: R
Length: 391 amino acids
Theoretical weight: 43.78 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P49146 (Residues: 2-381; Coverage: 100%)
Gene name: NPY2R
Pfam: 7 transmembrane receptor (rhodopsin family)
InterPro:
Neuropeptide Y receptor type 2 in PDB entry 7yoo, assembly 1, front view.
Neuropeptide Y receptor type 2 in PDB entry 7yoo, assembly 1, side view.
Neuropeptide Y receptor type 2 in PDB entry 7yoo, assembly 1, top view.
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single-chain antibody Fv fragment (scFv16)
Chain: S
Length: 259 amino acids
Theoretical weight: 27.78 KDa
Source organism: Mus musculus
Expression system: Trichoplusia ni
InterPro:
single-chain antibody Fv fragment (scFv16) in PDB entry 7yoo, assembly 1, front view.
single-chain antibody Fv fragment (scFv16) in PDB entry 7yoo, assembly 1, side view.
single-chain antibody Fv fragment (scFv16) in PDB entry 7yoo, assembly 1, top view.
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