1MMS

Crystal structure of the ribosomal PROTEIN L11-RNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A detailed view of a ribosomal active site: the structure of the L11-RNA complex.

Wimberly, B.T.Guymon, R.McCutcheon, J.P.White, S.W.Ramakrishnan, V.

(1999) Cell 97: 491-502

  • Also Cited By: 2BCW, 2GKZ, 2GKY, 1OLN

  • PubMed Abstract: 
  • We report the crystal structure of a 58 nucleotide fragment of 23S ribosomal RNA bound to ribosomal protein L11. This highly conserved ribonucleoprotein domain is the target for the thiostrepton family of antibiotics that disrupt elongation factor fu ...

    We report the crystal structure of a 58 nucleotide fragment of 23S ribosomal RNA bound to ribosomal protein L11. This highly conserved ribonucleoprotein domain is the target for the thiostrepton family of antibiotics that disrupt elongation factor function. The highly compact RNA has both familiar and novel structural motifs. While the C-terminal domain of L11 binds RNA tightly, the N-terminal domain makes only limited contacts with RNA and is proposed to function as a switch that reversibly associates with an adjacent region of RNA. The sites of mutations conferring resistance to thiostrepton and micrococcin line a narrow cleft between the RNA and the N-terminal domain. These antibiotics are proposed to bind in this cleft, locking the putative switch and interfering with the function of elongation factors.


    Related Citations: 
    • Site of Action of a Ribosomal RNA Methylase Conferring Resistance to Thiostrepton
      Thompson, J.,Schmidt, F.,Cundliffe, E.
      (1982) J.Biol.Chem. 257: 7915
    • Binding of Thiostrepton to a Complex of 23S RNA with Ribosomal Protein L11
      Thompson, J.,Cundliffe, E.,Stark, M.
      (1979) Eur.J.Biochem. 98: 261
    • Cooperative Interactions of RNA and Thiostrepton Antibiotic with Two Domains of Ribosomal Protein L11
      Xing, Y.,Draper, D.
      (1996) Biochemistry 35: 1581


    Organizational Affiliation

    Department of Biochemistry, University of Utah School of Medicine, Salt Lake City 84132, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (RIBOSOMAL PROTEIN L11)
A, B
140Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Mutation(s): 0 
Gene Names: rplK
Find proteins for P29395 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  P29395
Entity ID: 1
MoleculeChainsLengthOrganism
23S RIBOSOMAL RNAC,D58N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MMC
Query on MMC

Download SDF File 
Download CCD File 
A, C, D
METHYL MERCURY ION
C H3 Hg
DBUXSCUEGJMZAE-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
CD
Query on CD

Download SDF File 
Download CCD File 
A, C, D
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.890α = 90.00
b = 84.260β = 90.00
c = 155.510γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-04-17
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance