› 7dce

Electron Microscopy
3.8Å resolution

Cryo-EM structure of human XKR8-basigin complex bound to Fab fragment

Released:
DOI: 10.2210/pdb7dce/pdb
PDB entry 7dce coloured by chain, front view.
PDB entry 7dce coloured by chain, side view.
PDB entry 7dce coloured by chain, top view.
Source organisms:
Primary publication:
The tertiary structure of the human Xkr8-Basigin complex that scrambles phospholipids at plasma membranes.
Sakuragi T, Kanai R, Tsutsumi A, Narita H, Onishi E, Nishino K, Miyazaki T, Baba T, Kosako H, Nakagawa A, Kikkawa M, Toyoshima C, Nagata S
OpenAccess logo Nat Struct Mol Biol 28 825-834 (2021)
PMID: 34625749
Related structures: EMD-30636

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-211113 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Basigin Chain: B
Molecule details ›
Chain: B
Length: 176 amino acids
Theoretical weight: 19.59 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P35613 (Residues: 219-385; Coverage: 46%)
Gene names: BSG, UNQ6505/PRO21383
Sequence domains: Immunoglobulin domain
XK-related protein 8 Chain: X
Molecule details ›
Chain: X
Length: 405 amino acids
Theoretical weight: 45.98 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q9H6D3 (Residues: 1-395; Coverage: 100%)
Gene names: XKR8, XRG8
Sequence domains: XK-related protein
Heavy chain of Fab fragment Chain: H
Light chain of Fab fragment Chain: L

Ligands and Environments

1 bound ligand:
Ligand DLP 1 x DLP
1 modified residue:
Ligand PCA 1 x PCA

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 3.8Å
Relevant EMDB volumes: EMD-30636
Expression systems:
  • Spodoptera frugiperda
  • Homo sapiens

Quick links

Citations

3 review citations

XK-Associated McLeod Syndrome: Nonhematological Manifestations and Relation to VPS13A Disease.
Peikert et al. (2022)
2 more

5 mentions without citation

Regulation of phospholipid distribution in the lipid bilayer by flippases and scramblases.
Sakuragi et al. (2023)
4 more