1RL2

RIBOSOMAL PROTEIN L2 RNA-BINDING DOMAIN FROM BACILLUS STEAROTHERMOPHILUS

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

The three-dimensional structure of the RNA-binding domain of ribosomal protein L2; a protein at the peptidyl transferase center of the ribosome.

Nakagawa, A., Nakashima, T., Taniguchi, M., Hosaka, H., Kimura, M., Tanaka, I.

(1999) EMBO J 18: 1459-1467

  • DOI: 10.1093/emboj/18.6.1459
  • Primary Citation of Related Structures:  
    1RL2

  • PubMed Abstract: 

    • Ribosomal protein L2 is the largest protein component in the ribosome. It is located at or near the peptidyl transferase center and has been a prime candidate for the peptidyl transferase activity. It binds directly to 23S rRNA and plays a crucial role in its assembly ...

    Ribosomal protein L2 is the largest protein component in the ribosome. It is located at or near the peptidyl transferase center and has been a prime candidate for the peptidyl transferase activity. It binds directly to 23S rRNA and plays a crucial role in its assembly. The three-dimensional structure of the RNA-binding domain of L2 from Bacillus stearothermophilus has been determined at 2.3 A resolution by X-ray crystallography using the selenomethionyl MAD method. The RNA-binding domain of L2 consists of two recurring motifs of approximately 70 residues each. The N-terminal domain (positions 60-130) is homologous to the OB-fold, and the C-terminal domain (positions 131-201) is homologous to the SH3-like barrel. Residues Arg86 and Arg155, which have been identified by mutation experiments to be involved in the 23S rRNA binding, are located at the gate of the interface region between the two domains. The molecular architecture suggests how this important protein has evolved from the ancient nucleic acid-binding proteins to create a 23S rRNA-binding domain in the very remote past.

    Related Citations: 
    • Crystallization and preliminary X-ray crystallographic study of a 23S rRNA binding domain of the ribosomal protein L2 from Bacillus stearothermophilus
      Nakashima, T., Kimura, M., Nakagawa, A., Tanaka, I.
      (1998) J Struct Biol 124: 99
    Organizational Affiliation: 

    Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (RIBOSOMAL PROTEIN L2)A, B137Geobacillus stearothermophilusMutation(s): 0 
Gene Names: rplB
UniProt
Find proteins for P04257 (Geobacillus stearothermophilus)
Explore P04257 
Go to UniProtKB:  P04257
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04257
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		A, B L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.203 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 28.05α = 99.58
b = 36.19β = 95.86
c = 69.71γ = 102.63
Software Package:
Software NamePurpose
SHARPphasing
SOLOMONphasing
CNSrefinement
DENZOdata reduction
CCP4data scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-04-02
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-24
    Changes: Database references