› 5t16

X-ray diffraction
2.78Å resolution

Crystal structure of yeast RNase III (Rnt1p) complexed with a non-hydrolyzable RNA substrate analog

Released:
DOI: 10.2210/pdb5t16/pdb
PDB entry 5t16 coloured by chain, front view.
PDB entry 5t16 coloured by chain, side view.
PDB entry 5t16 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
The Functional Cycle of Rnt1p: Five Consecutive Steps of Double-Stranded RNA Processing by a Eukaryotic RNase III.
Song H, Fang X, Jin L, Shaw GX, Wang YX, Ji X
Structure 25 353-363 (2017)
PMID: 28111020

Function and Biology Details

Reaction catalysed: 
Endonucleolytic cleavage to 5'-phosphomonoester.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-169731 (preferred)
Entry contents:
2 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (3 distinct):
Ribonuclease 3 Chains: A, B, I, J
Molecule details ›
Chains: A, B, I, J
Length: 276 amino acids
Theoretical weight: 31.48 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: Q02555 (Residues: 184-459; Coverage: 59%)
Gene names: RNT1, YM9408.01C, YM9959.21, YMR239C
Sequence domains:
Ribonuclease 3 Chains: C, D, E, F, K, L, M, N
Molecule details ›
Chains: C, D, E, F, K, L, M, N
Length: 119 amino acids
Theoretical weight: 13.98 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: Q02555 (Residues: 41-159; Coverage: 25%)
Gene names: RNT1, YM9408.01C, YM9959.21, YMR239C
Sequence domains: Ribonuclease III N-terminal domain
RNA substrate analog Chains: G, H, O, P
Molecule details ›
Chains: G, H, O, P
Length: 34 nucleotides
Theoretical weight: 10.94 KDa

Ligands and Environments

1 bound ligand:
Ligand EDO 10 x EDO
1 modified residue:
Ligand 73W 4 x 73W

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P21
Unit cell:
a: 62.037Å b: 164.065Å c: 176.855Å
α: 90° β: 96.78° γ: 90°
R-values:
R R work R free
0.226 0.226 0.265
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Comparison of preribosomal RNA processing pathways in yeast, plant and human cells - focus on coordinated action of endo- and exoribonucleases.
Tomecki et al. (2017)
1 more

7 mentions without citation

A Glimpse of "Dicer Biology" Through the Structural and Functional Perspective.
Paturi et al. (2021)
6 more