4v74 | pdb_00004v74

70S-fMetVal-tRNAVal-tRNAfMet complex in hybrid pre-translocation state (pre5b)

Loading... Status: waiting for Mol* initialization Structural highlights 4v74 is a 10 chain structure with sequence from Escherichia coli K-12. This structure supersedes the now removed PDB entries 3j57 and 3j58. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: 4SU, 5MU, 6MZ, 7MG, ACE, CM0, FME, H2U, NH2, OMC, PSU, VAL Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function RS2_ECOLI 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 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Transfer RNA (tRNA)

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