› 2vpl

X-ray diffraction
2.3Å resolution

The structure of the complex between the first domain of L1 protein from Thermus thermophilus and mRNA from Methanococcus jannaschii

Released:
DOI: 10.2210/pdb2vpl/pdb
PDB entry 2vpl coloured by chain, front view.
PDB entry 2vpl coloured by chain, side view.
PDB entry 2vpl coloured by chain, top view.
Source organisms:
Primary publication:
Domain II of Thermus thermophilus ribosomal protein L1 hinders recognition of its mRNA.
Tishchenko S, Kljashtorny V, Kostareva O, Nevskaya N, Nikulin A, Gulak P, Piendl W, Garber M, Nikonov S
J Mol Biol 383 301-5 (2008)
PMID: 18778715

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-150941 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Large ribosomal subunit protein uL1 Chains: A, C
Molecule details ›
Chains: A, C
Length: 137 amino acids
Theoretical weight: 15.17 KDa
Source organism: Thermus thermophilus
Expression system: Escherichia coli
UniProt:
  • Canonical: P27150 (Residues: 2-229; Coverage: 60%)
Gene names: rpl1, rplA
Sequence domains: Ribosomal protein L1p/L10e family
Structure domains: 50S ribosomal protein L1; Chain A, Domain 1
FRAGMENT OF MRNA FOR L1-OPERON CONTAINING REGULATOR L1-BINDING SITE Chains: B, D
Molecule details ›
Chains: B, D
Length: 48 nucleotides
Theoretical weight: 15.52 KDa
Source organism: Methanocaldococcus jannaschii
Expression system: Escherichia coli

Ligands and Environments

1 bound ligand:
Ligand K 2 x K
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE BW7B
Spacegroup: P21212
Unit cell:
a: 76.1Å b: 144.35Å c: 56.16Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.212 0.209 0.274
Expression system: Escherichia coli

Quick links

Citations

2 review citations

RNA Structures as Mediators of Neurological Diseases and as Drug Targets.
Bernat et al. (2015)
1 more

6 mentions without citation

A nonredundant structure dataset for benchmarking protein-RNA computational docking.
Huang et al. (2013)
5 more