1I6U

RNA-PROTEIN INTERACTIONS: THE CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN S8/RRNA COMPLEX FROM METHANOCOCCUS JANNASCHII


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Detailed analysis of RNA-protein interactions within the ribosomal protein S8-rRNA complex from the archaeon Methanococcus jannaschii.

Tishchenko, S.Nikulin, A.Fomenkova, N.Nevskaya, N.Nikonov, O.Dumas, P.Moine, H.Ehresmann, B.Ehresmann, C.Piendl, W.Lamzin, V.Garber, M.Nikonov, S.

(2001) J.Mol.Biol. 311: 311-324

  • DOI: 10.1006/jmbi.2001.4877

  • PubMed Abstract: 
  • The crystal structure of ribosomal protein S8 bound to its target 16 S rRNA from a hyperthermophilic archaeon Methanococcus jannaschii has been determined at 2.6 A resolution. The protein interacts with the minor groove of helix H21 at two sites loca ...

    The crystal structure of ribosomal protein S8 bound to its target 16 S rRNA from a hyperthermophilic archaeon Methanococcus jannaschii has been determined at 2.6 A resolution. The protein interacts with the minor groove of helix H21 at two sites located one helical turn apart, with S8 forming a bridge over the RNA major groove. The specificity of binding is essentially provided by the C-terminal domain of S8 and the highly conserved nucleotide core, characterized by two dinucleotide platforms, facing each other. The first platform (A595-A596), which is the less phylogenetically and structurally constrained, does not directly contact the protein but has an important shaping role in inducing cross-strand stacking interactions. The second platform (U641-A642) is specifically recognized by the protein. The universally conserved A642 plays a pivotal role by ensuring the cohesion of the complex organization of the core through an array of hydrogen bonds, including the G597-C643-U641 base triple. In addition, A642 provides the unique base-specific interaction with the conserved Ser105, while the Thr106 - Thr107 peptide link is stacked on its purine ring. Noteworthy, the specific recognition of this tripeptide (Thr-Ser-Thr/Ser) is parallel to the recognition of an RNA tetraloop by a dinucleotide platform in the P4-P6 ribozyme domain of group I intron. This suggests a general dual role of dinucleotide platforms in recognition of RNA or peptide motifs. One prominent feature is that conserved side-chain amino acids, as well as conserved bases, are essentially involved in maintaining tertiary folds. The specificity of binding is mainly driven by shape complementarity, which is increased by the hydrophobic part of side-chains. The remarkable similarity of this complex with its homologue in the T. thermophilus 30 S subunit indicates a conserved interaction mode between Archaea and Bacteria.


    Related Citations: 
    • Crystal structure of ribosomal protein S8 from Thermus thermophilus reveals a high degree of structural conservation of a specific RNA binding site.
      Nevskaya, N.,Tishchenko, S.,Nikulin, A.,al-Karadaghi, S.,Liljas, A.,Ehresmann, B.,Ehresmann, C.,Garber, M.,Nikonov, S.
      (1998) J.Mol.Biol. 279: 233
    • NMR structure determination of the binding site for ribosomal protein S8 from Escherichia coli 16 S rRNA
      Kalurachci, K.,Nikonowicz, E.P.
      (1998) J.Mol.Biol. 280: 639


    Organizational Affiliation

    Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S8P
A, B
130Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)Gene Names: rps8
Find proteins for P54041 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Go to UniProtKB:  P54041
Entity ID: 1
MoleculeChainsLengthOrganism
16S RRNA FRAGMENTC,D37N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
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: 2.6 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.218 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 121.687α = 90.00
b = 121.687β = 90.00
c = 137.975γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
CCP4data scaling
MOSFLMdata reduction
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-08-03
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance