› 1y39

X-ray diffraction
2.8Å resolution

Co-evolution of protein and RNA structures within a highly conserved ribosomal domain

Released:
DOI: 10.2210/pdb1y39/pdb
PDB entry 1y39 coloured by chain, front view.
PDB entry 1y39 coloured by chain, side view.
PDB entry 1y39 coloured by chain, top view.
Source organisms:
Primary publication:
Coevolution of protein and RNA structures within a highly conserved ribosomal domain.
Dunstan MS, Guhathakurta D, Draper DE, Conn GL
Chem Biol 12 201-6 (2005)
PMID: 15734647

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-157429 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Large ribosomal subunit protein uL11 Chains: A, B
Molecule details ›
Chains: A, B
Length: 76 amino acids
Theoretical weight: 8.2 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P56210 (Residues: 58-133; Coverage: 57%)
Gene name: rplK
Sequence domains: Ribosomal protein L11, RNA binding domain
Structure domains: Ribosomal protein L11, C-terminal domain
58 Nucleotide Ribosomal 23S RNA Domain Chains: C, D
Molecule details ›
Chains: C, D
Length: 58 nucleotides
Theoretical weight: 18.86 KDa
Source organism: Escherichia coli
Expression system: Not provided
Sequence domains: Bacterial large subunit ribosomal RNA

Ligands and Environments

4 bound ligands:
Ligand 3CO 2 x 3CO
Ligand K 2 x K
Ligand MG 18 x MG
Ligand GOL 2 x GOL
1 modified residue:
Ligand GTP 2 x GTP

Experiments and Validation Details

Entry percentile scores
X-ray source: SRS BEAMLINE PX9.6
Spacegroup: P43212
Unit cell:
a: 150.24Å b: 150.24Å c: 62.984Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.22 0.22 0.253
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

5 citation in other articles

Structure of the thiostrepton resistance methyltransferase.S-adenosyl-L-methionine complex and its interaction with ribosomal RNA.
Dunstan et al. (2009)
4 more

2 mentions without citation

Describing RNA structure by libraries of clustered nucleotide doublets.
Sykes et al. (2005)
1 more