› 6s22

X-ray diffraction
1.96Å resolution

Crystal structure of the TgGalNAc-T3 in complex with UDP, manganese and FGF23c

Released:
DOI: 10.2210/pdb6s22/pdb
PDB entry 6s22 coloured by chain, front view.
PDB entry 6s22 coloured by chain, side view.
PDB entry 6s22 coloured by chain, top view.
Source organisms:
Primary publication:
Molecular basis for fibroblast growth factor 23 O-glycosylation by GalNAc-T3.
de Las Rivas M, Paul Daniel EJ, Narimatsu Y, Compañón I, Kato K, Hermosilla P, Thureau A, Ceballos-Laita L, Coelho H, Bernadó P, Marcelo F, Hansen L, Maeda R, Lostao A, Corzana F, Clausen H, Gerken TA, Hurtado-Guerrero R
Nat Chem Biol 16 351-360 (2020)
PMID: 31932717

Function and Biology Details

Reaction catalysed: 
UDP-N-acetyl-alpha-D-galactosamine + [protein]-L-serine = UDP + [protein]-3-O-(N-acetyl-alpha-D-galactosaminyl)-L-serine
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-124716 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Polypeptide N-acetylgalactosaminyltransferase 3 Chain: A
Molecule details ›
Chain: A
Length: 631 amino acids
Theoretical weight: 72.37 KDa
Source organism: Taeniopygia guttata
Expression system: Komagataella pastoris
UniProt:
  • Canonical: H0ZAB5 (Residues: 1-540, 541-616; Coverage: 100%)
Gene name: GALNT3
Sequence domains:
Fibroblast growth factor 23 C-terminal peptide Chain: F
Molecule details ›
Chain: F
Length: 12 amino acids
Theoretical weight: 1.41 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q9GZV9 (Residues: 170-181; Coverage: 5%)
Gene names: FGF23, HYPF, UNQ3027/PRO9828

Ligands and Environments

7 bound ligands:
Ligand EDO 14 x EDO
Ligand SO4 1 x SO4
Ligand UDP 1 x UDP
Ligand MN 1 x MN
Ligand NAG 1 x NAG
Ligand GOL 1 x GOL
Ligand NGA 1 x NGA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: P212121
Unit cell:
a: 50.957Å b: 104.823Å c: 143.466Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.18 0.179 0.216
Expression systems:
  • Komagataella pastoris
  • Not provided

Quick links

Citations

12 review citations

Global view of human protein glycosylation pathways and functions.
Schjoldager et al. (2020)
11 more

3 mentions without citation

Molecular basis for fibroblast growth factor 23 O-glycosylation by GalNAc-T3.
de Las Rivas et al. (2020)
2 more