› 6kam

X-ray diffraction
2.46Å resolution

Crystal structure of FKRP in complex with Ba ion, CDP-ribtol, and sugar acceptor

Released:
DOI: 10.2210/pdb6kam/pdb
PDB entry 6kam coloured by chain, front view.
PDB entry 6kam coloured by chain, side view.
PDB entry 6kam coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structures of fukutin-related protein (FKRP), a ribitol-phosphate transferase related to muscular dystrophy.
Kuwabara N, Imae R, Manya H, Tanaka T, Mizuno M, Tsumoto H, Kanagawa M, Kobayashi K, Toda T, Senda T, Endo T, Kato R
OpenAccess logo Nat Commun 11 303 (2020)
PMID: 31949166

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-190706 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Ribitol 5-phosphate transferase FKRP Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 455 amino acids
Theoretical weight: 50.03 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q9H9S5 (Residues: 45-495; Coverage: 91%)
Gene name: FKRP
Sequence domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, MAN, NGA
Carbohydrate polymer
6 bound ligands:
Ligand ZN 4 x ZN
Ligand NAG 7 x NAG
Ligand CDP 4 x CDP
Ligand RB0 4 x RB0
Ligand BA 4 x BA
Ligand PO4 2 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-17A
Spacegroup: P212121
Unit cell:
a: 78.571Å b: 119.24Å c: 254.646Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.21 0.208 0.249
Expression system: Homo sapiens

Quick links

Citations

4 review citations

Dystroglycanopathy: From Elucidation of Molecular and Pathological Mechanisms to Development of Treatment Methods.
Kanagawa M. (2021)
3 more

3 mentions without citation

NAD+ enhances ribitol and ribose rescue of α-dystroglycan functional glycosylation in human FKRP-mutant myotubes.
Ortiz-Cordero et al. (2021)
2 more