› 3am1

X-ray diffraction
2.4Å resolution

Crystal structure of O-Phosphoseryl-tRNA kinase complexed with anticodon-stem/loop truncated tRNA(Sec)

Released:
DOI: 10.2210/pdb3am1/pdb
PDB entry 3am1 coloured by chain, front view.
PDB entry 3am1 coloured by chain, side view.
PDB entry 3am1 coloured by chain, top view.
Source organism: Methanocaldococcus jannaschii
Primary publication:
C-terminal domain of archaeal O-phosphoseryl-tRNA kinase displays large-scale motion to bind the 7-bp D-stem of archaeal tRNA(Sec).
Sherrer RL, Araiso Y, Aldag C, Ishitani R, Ho JM, Söll D, Nureki O
Nucleic Acids Res 39 1034-41 (2011)
PMID: 20870747

Function and Biology Details

Reaction catalysed: 
ATP + L-seryl-tRNA(Sec) = ADP + O-phospho-L-seryl-tRNA(Sec)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-176715 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
L-seryl-tRNA(Sec) kinase Chain: A
Molecule details ›
Chain: A
Length: 260 amino acids
Theoretical weight: 31.01 KDa
Source organism: Methanocaldococcus jannaschii
Expression system: Escherichia coli
UniProt:
  • Canonical: Q58933 (Residues: 1-248; Coverage: 100%)
Gene names: MJ1538, pstK
Sequence domains: Chromatin associated protein KTI12
Structure domains:
ASL-truncated tRNA Chain: B
Molecule details ›
Chain: B
Length: 81 nucleotides
Theoretical weight: 26.19 KDa
Source organism: Methanocaldococcus jannaschii
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand ATP 1 x ATP
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P3112
Unit cell:
a: 46.749Å b: 46.749Å c: 459.712Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.232 0.229 0.292
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

4 review citations

Selenoproteins: molecular pathways and physiological roles.
Labunskyy et al. (2014)
3 more

9 mentions without citation

RNA folding pathways in stop motion.
Bottaro et al. (2016)
8 more