4PDB

CRYSTAL STRUCTURE OF BACILLUS ANTHRACIS RIBOSOMAL PROTEIN S8 IN COMPLEX WITH AN RNA APTAMER

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Structure analysis of free and bound states of an RNA aptamer against ribosomal protein S8 from Bacillus anthracis.

Davlieva, M., Donarski, J., Wang, J., Shamoo, Y., Nikonowicz, E.P.

(2014) Nucleic Acids Res 42: 10795-10808

  • DOI: https://doi.org/10.1093/nar/gku743
  • Primary Citation of Related Structures:  
    4PDB

  • PubMed Abstract: 

    • Several protein-targeted RNA aptamers have been identified for a variety of applications and although the affinities of numerous protein-aptamer complexes have been determined, the structural details of these complexes have not been widely explored. We examined the structural accommodation of an RNA aptamer that binds bacterial r-protein S8 ...

    Several protein-targeted RNA aptamers have been identified for a variety of applications and although the affinities of numerous protein-aptamer complexes have been determined, the structural details of these complexes have not been widely explored. We examined the structural accommodation of an RNA aptamer that binds bacterial r-protein S8. The core of the primary binding site for S8 on helix 21 of 16S rRNA contains a pair of conserved base triples that mold the sugar-phosphate backbone to S8. The aptamer, which does not contain the conserved sequence motif, is specific for the rRNA binding site of S8. The protein-free RNA aptamer adopts a helical structure with multiple non-canonical base pairs. Surprisingly, binding of S8 leads to a dramatic change in the RNA conformation that restores the signature S8 recognition fold through a novel combination of nucleobase interactions. Nucleotides within the non-canonical core rearrange to create a G-(G-C) triple and a U-(A-U)-U quartet. Although native-like S8-RNA interactions are present in the aptamer-S8 complex, the topology of the aptamer RNA differs from that of the helix 21-S8 complex. This is the first example of an RNA aptamer that adopts substantially different secondary structures in the free and protein-bound states and highlights the remarkable plasticity of RNA secondary structure.

    Organizational Affiliation: 

    Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77251-1892, USA edn@rice.edu.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8155Bacillus anthracis str. SterneMutation(s): 0 
Gene Names: rpsH
UniProt
Find proteins for Q81VR6 (Bacillus anthracis)
Explore Q81VR6 
Go to UniProtKB:  Q81VR6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ81VR6
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
SELEX RNA aptamerB [auth I]38synthetic construct
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.41α = 90
b = 59.27β = 90
c = 92.25γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement
PHENIXrefinement

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesRO1 AI080714
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesRO1 GM73969
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesU54 AI057156

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-03
    Type: Initial release
  • Version 1.1: 2014-10-01
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy
  • Version 1.3: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.4: 2019-12-11
    Changes: Author supporting evidence