› 3cul

X-ray diffraction
2.8Å resolution

Aminoacyl-tRNA synthetase ribozyme

Released:
DOI: 10.2210/pdb3cul/pdb
PDB entry 3cul coloured by chain, front view.
PDB entry 3cul coloured by chain, side view.
PDB entry 3cul coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis of specific tRNA aminoacylation by a small in vitro selected ribozyme.
Xiao H, Murakami H, Suga H, Ferré-D'Amaré AR
Nature 454 358-61 (2008)
PMID: 18548004

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-219237 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct RNA molecules
Macromolecules (3 distinct):
U1 small nuclear ribonucleoprotein A Chains: A, B
Molecule details ›
Chains: A, B
Length: 98 amino acids
Theoretical weight: 11.57 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P09012 (Residues: 1-98; Coverage: 35%)
Gene name: SNRPA
Sequence domains: RNA recognition motif
Structure domains: Alpha-Beta Plaits
RNA (92-MER) Chain: C
Molecule details ›
Chain: C
Length: 92 nucleotides
Theoretical weight: 29.82 KDa
Source organism: Homo sapiens
Expression system: CELL-FREE SYNTHESIS
RNA (92-MER) Chain: D
Molecule details ›
Chain: D
Length: 92 nucleotides
Theoretical weight: 29.66 KDa
Source organism: Homo sapiens
Expression system: CELL-FREE SYNTHESIS

Ligands and Environments

2 bound ligands:
Ligand MG 10 x MG
Ligand K 1 x K
2 modified residues:
Ligand GTP 1 x GTP
Ligand MSE 10 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: C2
Unit cell:
a: 192.151Å b: 48.725Å c: 90.515Å
α: 90° β: 93.5° γ: 90°
R-values:
R R work R free
0.227 0.227 0.283
Expression systems:
  • Escherichia coli
  • CELL-FREE SYNTHESIS

Quick links

Citations

24 review citations

Riboswitches: discovery of drugs that target bacterial gene-regulatory RNAs.
Deigan et al. (2011)
23 more

6 mentions without citation

Use of the spliceosomal protein U1A to facilitate crystallization and structure determination of complex RNAs.
Ferré-D'Amaré AR. (2010)
5 more