1ZC8

Coordinates of tmRNA, SmpB, EF-Tu and h44 fitted into Cryo-EM map of the 70S ribosome and tmRNA complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 13 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Visualizing tmRNA Entry into a Stalled Ribosome

Valle, M.Gillet, R.Kaur, S.Henne, A.Ramakrishnan, V.Frank, J.

(2003) Science 300: 127-130

  • DOI: 10.1126/science.1081798

  • PubMed Abstract: 
  • Bacterial ribosomes stalled on defective messenger RNAs (mRNAs) are rescued by tmRNA, an approximately 300-nucleotide-long molecule that functions as both transfer RNA (tRNA) and mRNA. Translation then switches from the defective message to a short o ...

    Bacterial ribosomes stalled on defective messenger RNAs (mRNAs) are rescued by tmRNA, an approximately 300-nucleotide-long molecule that functions as both transfer RNA (tRNA) and mRNA. Translation then switches from the defective message to a short open reading frame on tmRNA that tags the defective nascent peptide chain for degradation. However, the mechanism by which tmRNA can enter and move through the ribosome is unknown. We present a cryo-electron microscopy study at approximately 13 to 15 angstroms of the entry of tmRNA into the ribosome. The structure reveals how tmRNA could move through the ribosome despite its complicated topology and also suggests roles for proteins S1 and SmpB in the function of tmRNA.


    Related Citations: 
    • Cryo-EM reveals an active role for aminoacyl-tRNA in the accommodation process
      Valle, M.,Sengupta, J.,Swami, N.K.,Grassucci, R.A.,Burkhardt, N.,Nierhaus, K.H.,Agrawal, R.K.,Frank, J.
      (2002) Embo J. 21: 3557
    • Structure of small protein B: the protein component of the tmRNA SmpB system for ribosome rescue
      Dong, G.,Nowakowski, J.,Hoffman, D.W.
      (2002) Embo J. 21: 1845
    • tmRDB (tmRNA database)
      Knudsen, B.,Wower, J.,Zwieb, C.,Gorodkin, J.
      (2001) Nucleic Acids Res. 29: 171
    • Selection of tRNA by the Ribosome Requires a Transition from an Open to a Closed Form
      Ogle, J.M.,Murphy Iv, F.V.,Tarry, M.J.,Ramakrishnan, V.
      (2002) Cell 111: 721
    • E. Coli Cysteinyl-tRNA and T. Aquaticus Elongation Factor Ef-Tu: GTP Ternary Complex
      Nissen, P.,Kjeldgaard, M.,Thirup, S.,Nyborg, J.
      (1999) Structure Fold.Des. 7: 143


    Organizational Affiliation

    Howard Hughes Medical Institute, Wadsworth Center, Health Research, Inc., Empire State Plaza, Albany, NY 12201-0509, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
SsrA-binding protein
K
130Aquifex aeolicus (strain VF5)Mutation(s): 0 
Gene Names: smpB (smb)
Find proteins for O66640 (Aquifex aeolicus (strain VF5))
Go to UniProtKB:  O66640
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Elongation factor Tu
Y
405Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: tufA (tuf)
Find proteins for Q5SHN6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN6
Entity ID: 1
MoleculeChainsLengthOrganism
TLD 16S ribosomal RNAA59Thermus thermophilus
Entity ID: 2
MoleculeChainsLengthOrganism
H2 16S rRNAB16Thermus thermophilus
Entity ID: 3
MoleculeChainsLengthOrganism
H2b d mRNAC31Thermus thermophilus
Entity ID: 4
MoleculeChainsLengthOrganism
protein kinase 4 mRNAG30Thermus thermophilus
Entity ID: 5
MoleculeChainsLengthOrganism
H5 16S ribosomal RNAF29Thermus thermophilus
Entity ID: 6
MoleculeChainsLengthOrganism
protein kinase 2 mRNAH59Thermus thermophilus
Entity ID: 7
MoleculeChainsLengthOrganism
protein kinase 3I49Thermus thermophilus
Entity ID: 8
MoleculeChainsLengthOrganism
protein kinase 4 mRNAJ52Thermus thermophilus
Entity ID: 9
MoleculeChainsLengthOrganism
H44 16S ribosomal RNAZ91Thermus thermophilus
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 13 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-04-19
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2013-12-11
    Type: Structure summary