4v6z

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E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in classic pre-translocation state (pre1b)

Structural highlights

4v6z is a 10 chain structure with sequence from Escherichia coli K-12. This structure supersedes the now removed PDB entries 3j4w and 3j4x. 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

RL1_ECOLI One of the primary rRNA binding proteins, it binds very close to the 3'-end of the 23S rRNA. Forms part of the L1 stalk. It is often not seen in high-resolution crystal structures, but can be seen in cryo_EM and 3D reconstruction models. These indicate that the distal end of the stalk moves by approximately 20 angstroms (PubMed:12859903). This stalk movement is thought to be coupled to movement of deacylated tRNA into and out of the E site, and thus to participate in tRNA translocation (PubMed:12859903). Contacts the P and E site tRNAs.[HAMAP-Rule:MF_01318_B] Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA.[HAMAP-Rule:MF_01318_B]

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[1]

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

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See Also

References

  1. ↑ 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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4v6z, resolution 12.00Å

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