4v73

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E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in hybrid pre-translocation state (pre5a)

Structural highlights

4v73 is a 10 chain structure with sequence from Escherichia coli K-12. This structure supersedes the now removed PDB entries 3j55 and 3j56. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Experimental data:Check to display Experimental Data
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RS13_ECOLI Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA.[1] In the E.coli 70S ribosome in the initiation state (PubMed:12809609) was modeled to contact the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; bridge B1a is broken in the model with bound EF-G, while the protein-protein contacts between S13 and L5 in B1b change (PubMed:12809609). The 23S rRNA contact site in bridge B1a is modeled to differ in different ribosomal states (PubMed:16272117), contacting alternately S13 or S19. In the two 3.5 angstroms resolved ribosome structures (PubMed:12859903) the contacts between L5, S13 and S19 bridge B1b are different, confirming the dynamic nature of this interaction. Bridge B1a is not visible in the crystallized ribosomes due to 23S rRNA disorder.[2] Contacts the tRNAs in the A and P sites.[3] The C-terminal tail plays a role in the affinity of the 30S P site for different tRNAs.[4]

Publication Abstract from PubMed

During protein synthesis, tRNAs move from the ribosome's aminoacyl to peptidyl to exit sites. Here we investigate conformational motions during spontaneous translocation, using molecular dynamics simulations of 13 intermediate-translocation-state models obtained by combining Escherichia coli ribosome crystal structures with cryo-EM data. Resolving fast transitions between states, we find that tRNA motions govern the transition rates within the pre- and post-translocation states. Intersubunit rotations and L1-stalk motion exhibit fast intrinsic submicrosecond dynamics. The L1 stalk drives the tRNA from the peptidyl site and links intersubunit rotation to translocation. Displacement of tRNAs is controlled by 'sliding' and 'stepping' mechanisms involving conserved L16, L5 and L1 residues, thus ensuring binding to the ribosome despite large-scale tRNA movement. Our results complement structural data with a time axis, intrinsic transition rates and molecular forces, revealing correlated functional motions inaccessible by other means.

Energy barriers and driving forces in tRNA translocation through the ribosome.,Bock LV, Blau C, Schroder GF, Davydov II, Fischer N, Stark H, Rodnina MV, Vaiana AC, Grubmuller H Nat Struct Mol Biol. 2013 Nov 3. doi: 10.1038/nsmb.2690. PMID:24186064[5]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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See Also

References

  1. ↑ Hoang L, Fredrick K, Noller HF. Creating ribosomes with an all-RNA 30S subunit P site. Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12439-43. Epub 2004 Aug 12. PMID:15308780 doi:10.1073/pnas.0405227101
  2. ↑ Hoang L, Fredrick K, Noller HF. Creating ribosomes with an all-RNA 30S subunit P site. Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12439-43. Epub 2004 Aug 12. PMID:15308780 doi:10.1073/pnas.0405227101
  3. ↑ Hoang L, Fredrick K, Noller HF. Creating ribosomes with an all-RNA 30S subunit P site. Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12439-43. Epub 2004 Aug 12. PMID:15308780 doi:10.1073/pnas.0405227101
  4. ↑ Hoang L, Fredrick K, Noller HF. Creating ribosomes with an all-RNA 30S subunit P site. Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12439-43. Epub 2004 Aug 12. PMID:15308780 doi:10.1073/pnas.0405227101
  5. ↑ Bock LV, Blau C, Schroder GF, Davydov II, Fischer N, Stark H, Rodnina MV, Vaiana AC, Grubmuller H. Energy barriers and driving forces in tRNA translocation through the ribosome. Nat Struct Mol Biol. 2013 Nov 3. doi: 10.1038/nsmb.2690. PMID:24186064 doi:http://dx.doi.org/10.1038/nsmb.2690

Contents


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4v73, resolution 15.00Å

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