6PRV

58nt RNA L11-binding domain from E. coli 23S rRNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Ribosomal protein L11 selectively stabilizes a tertiary structure of the GTPase Center rRNA domain.

Welty, R.Rau, M.Pabit, S.Dunstan, M.S.Conn, G.L.Pollack, L.Hall, K.B.

(2019) J.Mol.Biol. --: --

  • DOI: 10.1016/j.jmb.2019.12.010

  • PubMed Abstract: 
  • The GTPase Center (GAC) RNA domain in bacterial 23S rRNA is directly bound by ribosomal protein L11, and this complex is essential to ribosome function. Previous cocrystal structures of the 58-nucleotide GAC RNA bound to L11 revealed the intricate te ...

    The GTPase Center (GAC) RNA domain in bacterial 23S rRNA is directly bound by ribosomal protein L11, and this complex is essential to ribosome function. Previous cocrystal structures of the 58-nucleotide GAC RNA bound to L11 revealed the intricate tertiary fold of the RNA domain, with one monovalent and several divalent ions located in specific sites within the structure. Here, we report a new crystal structure of the free GAC that is essentially identical to the L11-bound structure, which retains many common sites of divalent ion occupation. This new structure demonstrates that RNA alone folds into its tertiary structure with bound divalent ions. In solution, we find that this tertiary structure is not static, but rather is best described as an ensemble of states. While L11 protein cannot bind to the GAC until the RNA has adopted its tertiary structure, new experimental data show that L11 binds to Mg 2+ -dependent folded states, which we suggest lie along the folding pathway of the RNA. We propose that L11 stabilizes a specific GAC RNA tertiary state, corresponding to the crystal structure, and that this structure reflects the functionally critical conformation of the rRNA domain in the fully assembled ribosome.


    Organizational Affiliation

    School of Applied and Engineering Physics, Cornell University, Clark Hall, Ithaca, NY, 14853, USA.,Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S Euclid Ave, St Louis, MO, 63110, USA; Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S Euclid Ave, St Louis, MO, 63110, USA. Electronic address: kathleenhal@gmail.com.,Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom.,Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta GA, 30322, USA.,Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S Euclid Ave, St Louis, MO, 63110, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
23S rRNAA,B,C,D58Escherichia coli
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B, C
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
GTP
Query on GTP
A, B, C, D
NON-POLYMERC10 H16 N5 O14 P3G
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.204 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 89.610α = 90.00
b = 73.610β = 100.96
c = 130.280γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-01-08
    Type: Initial release