PDBsum entry 3qkf

Isomerase

PDB id: 3qkf

Contents

Protein chains

(+ 2 more) 393 a.a.

Ligands

GCO ×8

Metals

_MG ×8

Waters ×3178

References listed in PDB file

Key reference

• Title: A new tRNA intermediate revealed on the ribosome during ef4-Mediated back-Translocation.
• Authors: S.R.Connell, M.Topf, Y.Qin, D.N.Wilson, T.Mielke, P.Fucini, K.H.Nierhaus, C.M.Spahn.
• Ref.: Nat Struct Biol, 2008, 15, 910-915.
• PubMed id: 19172743

Abstract

EF4 (LepA) is an almost universally conserved translational GTPase in eubacteria. It seems to be essential under environmental stress conditions and has previously been shown to back-translocate the tRNAs on the ribosome, thereby reverting the canonical translocation reaction. In the current work, EF4 was directly visualized in the process of back-translocating tRNAs by single-particle cryo-EM. Using flexible fitting methods, we built a model of ribosome-bound EF4 based on the cryo-EM map and a recently published unbound EF4 X-ray structure. The cryo-EM map establishes EF4 as a noncanonical elongation factor that interacts not only with the elongating ribosome, but also with the back-translocated tRNA in the A-site region, which is present in a previously unseen, intermediate state and deviates markedly from the position of a canonical A-tRNA. Our results, therefore, provide insight into the underlying structural principles governing back-translocation.