› 3vbb

X-ray diffraction
2.89Å resolution

Crystal Structure of Seryl-tRNA Synthetase from Human at 2.9 angstroms

Released:
DOI: 10.2210/pdb3vbb/pdb
PDB entry 3vbb coloured by chain, front view.
PDB entry 3vbb coloured by chain, side view.
PDB entry 3vbb coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Unique domain appended to vertebrate tRNA synthetase is essential for vascular development.
Xu X, Shi Y, Zhang HM, Swindell EC, Marshall AG, Guo M, Kishi S, Yang XL
Nat Commun 3 681 (2012)
PMID: 22353712

Function and Biology Details

Reaction catalysed: 
ATP + L-serine + tRNA(Sec) = AMP + diphosphate + L-seryl-tRNA(Sec)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-155961 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Serine--tRNA ligase, cytoplasmic Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 522 amino acids
Theoretical weight: 59.93 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P49591 (Residues: 1-514; Coverage: 100%)
Gene names: SARS, SARS1, SERS
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand MG 2 x MG
Ligand PO4 6 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL7-1
Spacegroup: P212121
Unit cell:
a: 116.8Å b: 189.417Å c: 230.589Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.197 0.194 0.25
Expression system: Escherichia coli

Quick links

Citations

11 review citations

Essential nontranslational functions of tRNA synthetases.
Guo et al. (2013)
10 more

5 mentions without citation

Structural disorder in expanding the functionome of aminoacyl-tRNA synthetases.
Yang XL. (2013)
4 more