› 5zlg

X-ray diffraction
2.8Å resolution

Human duodenal cytochrome b (Dcytb) in zinc ion and ascorbate bound form

Released:
DOI: 10.2210/pdb5zlg/pdb
PDB entry 5zlg coloured by chain, front view.
PDB entry 5zlg coloured by chain, side view.
PDB entry 5zlg coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis for promotion of duodenal iron absorption by enteric ferric reductase with ascorbate.
Ganasen M, Togashi H, Takeda H, Asakura H, Tosha T, Yamashita K, Hirata K, Nariai Y, Urano T, Yuan X, Hamza I, Mauk AG, Shiro Y, Sugimoto H, Sawai H
Commun Biol 1 120 (2018)
PMID: 30272000

Function and Biology Details

Reaction catalysed: 
Ascorbate(Side 1) + Fe(III)(Side 2) = monodehydroascorbate(Side 1) + Fe(II)(Side 2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-176116 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Plasma membrane ascorbate-dependent reductase CYBRD1 Chain: A
Molecule details ›
Chain: A
Length: 292 amino acids
Theoretical weight: 32.36 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q53TN4 (Residues: 1-286; Coverage: 100%)
Gene names: CYBRD1, DCYTB, FRRS3
Sequence domains: Eukaryotic cytochrome b561

Ligands and Environments

3 bound ligands:
Ligand HEM 2 x HEM
Ligand ZN 1 x ZN
Ligand ASC 2 x ASC
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL32XU
Spacegroup: C2
Unit cell:
a: 65.18Å b: 115.57Å c: 48.6Å
α: 90° β: 118.44° γ: 90°
R-values:
R R work R free
0.208 0.206 0.252
Expression system: Escherichia coli

Quick links

Citations

7 review citations

Iron homeostasis and organismal aging.
Zeidan et al. (2021)
6 more

4 mentions without citation

Haem is crucial for medium-dependent metronidazole resistance in clinical isolates of Clostridioides difficile.
Boekhoud et al. (2021)
3 more