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: 13.0 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
  • Primary Citation of Related Structures:  
    1ZC8

  • 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 open reading frame on tmRNA that tags the defective nascent peptide chain for degradation ...

    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: 
    • 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
    • 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
    • E. Coli Cysteinyl-tRNA and T. Aquaticus Elongation Factor Ef-Tu: GTP Ternary Complex
      Nissen, P., Kjeldgaard, M., Thirup, S., Nyborg, J.
      (1999) Structure 7: 143
    • 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

    Organizational Affiliation

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



Macromolecules

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
SsrA-binding proteinJ [auth K]130Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for O66640 (Aquifex aeolicus (strain VF5))
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Go to UniProtKB:  O66640
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UniProt GroupO66640
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Elongation factor TuK [auth Y]405Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for Q5SHN6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SHN6 
Go to UniProtKB:  Q5SHN6
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UniProt GroupQ5SHN6
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Entity ID: 1
MoleculeChainsLengthOrganismImage
TLD 16S ribosomal RNAA59Thermus thermophilus
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Entity ID: 2
MoleculeChainsLengthOrganismImage
H2 16S rRNAB16Thermus thermophilus
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Entity ID: 3
MoleculeChainsLengthOrganismImage
H2b d mRNAC31Thermus thermophilus
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Entity ID: 4
MoleculeChainsLengthOrganismImage
protein kinase 4 mRNAD [auth G]30Thermus thermophilus
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Entity ID: 5
MoleculeChainsLengthOrganismImage
H5 16S ribosomal RNAE [auth F]29Thermus thermophilus
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Entity ID: 6
MoleculeChainsLengthOrganismImage
protein kinase 2 mRNAF [auth H]59Thermus thermophilus
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Entity ID: 7
MoleculeChainsLengthOrganismImage
protein kinase 3G [auth I]49Thermus thermophilus
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Entity ID: 8
MoleculeChainsLengthOrganismImage
protein kinase 4 mRNAH [auth J]52Thermus thermophilus
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Entity ID: 9
MoleculeChainsLengthOrganismImage
H44 16S ribosomal RNAI [auth Z]91Thermus thermophilus
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 13.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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