3RF2

Crystal Structure of 30S Ribosomal Protein S8 from Aquifex Aeolicus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The Structure of Aquifex aeolicus Ribosomal Protein S8 Reveals a Unique Subdomain that Contributes to an Extremely Tight Association with 16S rRNA.

Menichelli, E.Edgcomb, S.P.Recht, M.I.Williamson, J.R.

(2012) J.Mol.Biol. 415: 489-502

  • DOI: 10.1016/j.jmb.2011.10.046

  • PubMed Abstract: 
  • The assembly of ribonucleoprotein complexes occurs under a broad range of conditions, but the principles that promote assembly and allow function at high temperature are poorly understood. The ribosomal protein S8 from Aquifex aeolicus (AS8) is uniqu ...

    The assembly of ribonucleoprotein complexes occurs under a broad range of conditions, but the principles that promote assembly and allow function at high temperature are poorly understood. The ribosomal protein S8 from Aquifex aeolicus (AS8) is unique in that there is a 41-residue insertion in the consensus S8 sequence. In addition, AS8 exhibits an unusually high affinity for the 16S ribosomal RNA, characterized by a picomolar dissociation constant that is approximately 26,000-fold tighter than the equivalent interaction from Escherichia coli. Deletion analysis demonstrated that binding to the minimal site on helix 21 occurred at the same nanomolar affinity found for other bacterial species. The additional affinity required the presence of a three-helix junction between helices 20, 21, and 22. The crystal structure of AS8 was solved, revealing the helix-loop-helix geometry of the unique AS8 insertion region, while the core of the molecule is conserved with known S8 structures. The AS8 structure was modeled onto the structure of the 30S ribosomal subunit from E. coli, suggesting the possibility that the unique subdomain provides additional backbone and side-chain contacts between the protein and an unpaired base within the three-way junction of helices 20, 21, and 22. Point mutations in the protein insertion subdomain resulted in a significantly reduced RNA binding affinity with respect to wild-type AS8. These results indicate that the AS8-specific subdomain provides additional interactions with the three-way junction that contribute to the extremely tight binding to ribosomal RNA.


    Organizational Affiliation

    Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
A
168Aquifex aeolicus (strain VF5)Gene Names: rpsH
Find proteins for O67566 (Aquifex aeolicus (strain VF5))
Go to UniProtKB:  O67566
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.223 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 96.235α = 90.00
b = 96.235β = 90.00
c = 37.614γ = 90.00
Software Package:
Software NamePurpose
SOLVEphasing
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
RESOLVEphasing
PDB_EXTRACTdata extraction
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-16
    Type: Initial release
  • Version 1.1: 2011-12-14
    Type: Database references
  • Version 1.2: 2012-02-01
    Type: Database references
  • Version 1.3: 2017-10-25
    Type: Advisory, Author supporting evidence