4V71
E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate pre-translocation state (pre2)
This is a non-PDB format compatible entry.
Summary for 4V71
| Entry DOI | 10.2210/pdb4v71/pdb |
| Related | 3J4V 3J4W 3J4X 3J4Y 3J51 3J52 3J53 3J54 3J55 3J56 3J57 3J58 3J59 3J5A 3J5B 3J5C 3J5D 3J5E 3J5F 3J5G 3J5H 3J5I 3J5J 3J5K |
| EMDB information | 1716 1717 1718 1719 1720 1721 1722 1723 1724 2472 2473 2474 2475 |
| Descriptor | 30S ribosomal protein S2, 30S ribosomal protein S11, 30S ribosomal protein S12, ... (58 entities in total) |
| Functional Keywords | cryo-em refinement, trna, translocation intermediate, ribosome |
| Biological source | Escherichia coli More |
| Total number of polymer chains | 56 |
| Total formula weight | 2195471.29 |
| Authors | Blau, C.,Bock, L.V.,Schroder, G.F.,Davydov, I.,Fischer, N.,Stark, H.,Rodnina, M.V.,Vaiana, A.C.,Grubmuller, H. (deposition date: 2013-10-14, release date: 2014-07-09, Last modification date: 2024-11-20) |
| Primary citation | Bock, L.V.,Blau, C.,Schroder, G.F.,Davydov, I.I.,Fischer, N.,Stark, H.,Rodnina, M.V.,Vaiana, A.C.,Grubmuller, H. Energy barriers and driving forces in tRNA translocation through the ribosome. Nat.Struct.Mol.Biol., 20:1390-1396, 2013 Cited by PubMed Abstract: 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. PubMed: 24186064DOI: 10.1038/nsmb.2690 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (20 Å) |
Structure validation
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