› 8ybb

X-ray diffraction
3.12Å resolution

Crystal structure of the sigma-1 receptor from Xenopus laevis with side opening

Released:
DOI: 10.2210/pdb8ybb/pdb
PDB entry 8ybb coloured by chain, front view.
PDB entry 8ybb coloured by chain, side view.
PDB entry 8ybb coloured by chain, top view.
Source organism: Xenopus laevis
Primary publication:
Insight into binding of endogenous neurosteroid ligands to the sigma-1 receptor.
Fu C, Xiao Y, Zhou X, Sun Z
OpenAccess logo Nat Commun 15 5619 (2024)
PMID: 38965213

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-179508 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Sigma non-opioid intracellular receptor 1 Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 233 amino acids
Theoretical weight: 25.72 KDa
Source organism: Xenopus laevis
Expression system: Komagataella pastoris
UniProt:
  • Canonical: Q6DCU6 (Residues: 1-221; Coverage: 100%)
Gene names: oprs1, sigmar1
Sequence domains: ERG2 and Sigma1 receptor like protein

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: C2
Unit cell:
a: 86.901Å b: 146.848Å c: 145.804Å
α: 90° β: 107.01° γ: 90°
R-values:
R R work R free
0.237 0.235 0.267
Expression system: Komagataella pastoris

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