› 1r3e

X-ray diffraction
2.1Å resolution

Crystal Structure of tRNA Pseudouridine Synthase TruB and Its RNA Complex: RNA-protein Recognition Through a Combination of Rigid Docking and Induced Fit

Released:
DOI: 10.2210/pdb1r3e/pdb
PDB entry 1r3e coloured by chain, front view.
PDB entry 1r3e coloured by chain, side view.
PDB entry 1r3e coloured by chain, top view.
Source organism: Thermotoga maritima
Primary publication:
Structure of tRNA pseudouridine synthase TruB and its RNA complex: RNA recognition through a combination of rigid docking and induced fit.
Pan H, Agarwalla S, Moustakas DT, Finer-Moore J, Stroud RM
Proc Natl Acad Sci U S A 100 12648-53 (2003)
PMID: 14566049

Function and Biology Details

Reaction catalysed: 
tRNA uridine(55) = tRNA pseudouridine(55)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-194645 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct RNA molecules
Macromolecules (3 distinct):
tRNA pseudouridine synthase B Chain: A
Molecule details ›
Chain: A
Length: 309 amino acids
Theoretical weight: 35.52 KDa
Source organism: Thermotoga maritima
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9WZW0 (Residues: 1-309; Coverage: 100%)
Gene names: TM_0856, truB
Sequence domains:
Structure domains:
5'-R(*CP*UP*GP*UP*GP*UP*(FHU)P*CP*GP*AP*UP*CP*CP*AP*CP*AP*G)-3' Chain: C
Molecule details ›
Chain: C
Length: 17 nucleotides
Theoretical weight: 5.42 KDa
Source organism: Thermotoga maritima
Expression system: Not provided
5'-R(*CP*UP*GP*UP*GP*UP*UP*CP*GP*AP*UP*CP*CP*AP*CP*AP*G)-3' Chains: D, E
Molecule details ›
Chains: D, E
Length: 17 nucleotides
Theoretical weight: 5.38 KDa
Source organism: Thermotoga maritima
Expression system: Not provided

Ligands and Environments

No bound ligands
1 modified residue:
Ligand FHU 1 x FHU

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.3.1
Spacegroup: C2
Unit cell:
a: 98.862Å b: 159.337Å c: 44.545Å
α: 90° β: 97.77° γ: 90°
R-values:
R R work R free
0.223 0.223 0.273
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

17 review citations

Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go.
Moitessier et al. (2008)
16 more

19 mentions without citation

A structural perspective of RNA recognition by intrinsically disordered proteins.
Basu et al. (2016)
18 more