› 8dti

Electron Microscopy
3.8Å resolution

Cryo-EM structure of Arabidopsis SPY in complex with GDP-fucose

Released:
DOI: 10.2210/pdb8dti/pdb
PDB entry 8dti coloured by chain, front view.
PDB entry 8dti coloured by chain, side view.
PDB entry 8dti coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Cryo-EM structure of the full length Arabidopsis SPY with complete TPRs
Kumar S, Zhou Y
Nat Commun (2023)
Related structures: EMD-27699

Function and Biology Details

Reactions catalysed: 
GDP-beta-L-fucose + [protein]-(L-serine/L-threonine) = GDP + [protein]-3-O-(alpha-L-fucosyl)-(L-serine/L-threonine)
UDP-N-acetyl-alpha-D-glucosamine + [protein]-L-serine = UDP + [protein]-3-O-(N-acetyl-beta-D-glucosaminyl)-L-serine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-188302 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Probable UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase SPINDLY Chains: A, B
Molecule details ›
Chains: A, B
Length: 946 amino acids
Theoretical weight: 105.28 KDa
Source organism: Arabidopsis thaliana
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q96301 (Residues: 1-914; Coverage: 100%)
Gene names: At3g11540, F24K9.29, SPY
Sequence domains:

Ligands and Environments

1 bound ligand:
Ligand GFB 2 x GFB
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.8Å
Relevant EMDB volumes: EMD-27699
Expression system: Spodoptera frugiperda

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