› 5apg

X-ray diffraction
1.6Å resolution

Structure of the SAM-dependent rRNA:acp-transferase Tsr3 from Vulcanisaeta distributa

Released:
DOI: 10.2210/pdb5apg/pdb
PDB entry 5apg coloured by chain, front view.
PDB entry 5apg coloured by chain, side view.
PDB entry 5apg coloured by chain, top view.
Source organism: Vulcanisaeta distributa DSM 14429
Primary publication:
Ribosome biogenesis factor Tsr3 is the aminocarboxypropyl transferase responsible for 18S rRNA hypermodification in yeast and humans.
Meyer B, Wurm JP, Sharma S, Immer C, Pogoryelov D, Kötter P, Lafontaine DL, Wöhnert J, Entian KD
Nucleic Acids Res 44 4304-16 (2016)
PMID: 27084949

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-122793 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
16S rRNA aminocarboxypropyltransferase Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 185 amino acids
Theoretical weight: 21.14 KDa
Source organism: Vulcanisaeta distributa DSM 14429
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: E1QU22 (Residues: 1-185; Coverage: 100%)
Gene name: Vdis_0418
Sequence domains: Ribosome biogenesis protein, C-terminal

Ligands and Environments

2 bound ligands:
Ligand EEM 3 x EEM
Ligand MES 3 x MES
1 modified residue:
Ligand MSE 12 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: C2
Unit cell:
a: 115.95Å b: 66.97Å c: 106.42Å
α: 90° β: 89.99° γ: 90°
R-values:
R R work R free
0.193 0.193 0.203
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

10 review citations

Tuning the ribosome: The influence of rRNA modification on eukaryotic ribosome biogenesis and function.
Sloan et al. (2017)
9 more

4 mentions without citation

S-Adenosylmethionine: more than just a methyl donor.
Lee et al. (2023)
3 more