› 8yn3

Electron Microscopy
2.56Å resolution

Cryo-EM structure of histamine H2 receptor in complex with histamine and miniGs

Released:
DOI: 10.2210/pdb8yn3/pdb
PDB entry 8yn3 coloured by chain, front view.
PDB entry 8yn3 coloured by chain, side view.
PDB entry 8yn3 coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of ligand recognition and activation of the histamine receptor family.
Zhang X, Liu G, Zhong YN, Zhang R, Yang CC, Niu C, Pu X, Sun J, Zhang T, Yang L, Zhang C, Li X, Shen X, Xiao P, Sun JP, Gong W
Nat Commun 15 8296 (2024)
PMID: 39333117
Related structures: EMD-39413

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
PDBe Complex ID:
PDB-CPX-279874 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
Engineered guanine nucleotide,binding protein G(s) subunit alpha Chain: A
Molecule details ›
Chain: A
Length: 246 amino acids
Theoretical weight: 29.05 KDa
Source organism: synthetic construct
Expression system: Spodoptera frugiperda
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 Chain: B
Molecule details ›
Chain: B
Length: 376 amino acids
Theoretical weight: 40.85 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
Nanobody Nb35 Chain: N
Molecule details ›
Chain: N
Length: 138 amino acids
Theoretical weight: 15.14 KDa
Source organism: synthetic construct
Expression system: Escherichia coli
Histamine H2 receptor Chain: R
Molecule details ›
Chain: R
Length: 568 amino acids
Theoretical weight: 62.47 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P25021 (Residues: 1-312; Coverage: 87%)
Gene name: HRH2
Sequence domains: 7 transmembrane receptor (rhodopsin family)

Ligands and Environments

2 bound ligands:
Ligand HSM 1 x HSM
Ligand CLR 1 x CLR
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.56Å
Relevant EMDB volumes: EMD-39413
Expression systems:
  • Spodoptera frugiperda
  • Escherichia coli

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