1NJM

The crystal structure of the 50S Large ribosomal subunit from Deinococcus radiodurans complexed with a tRNA acceptor stem mimic (ASM) and the antibiotic sparsomycin

Summary for 1NJM

• Entry DOI: 10.2210/pdb1njm/pdb
• Related: 1JZX 1JZY 1JZZ 1K00 1K01 1NJN 1NJO 1NJP 1NKW
• Descriptor: 23S ribosomal RNA, tRNA acceptor stem mimic, 50S ribosomal protein L16, ... (5 entities in total)
• Functional Keywords: ribosomes, trna, puromycin, sparsomycin, peptidyl-transferase, peptide bond formation, ribosome
• Biological source: Deinococcus radiodurans; More
• Total number of polymer chains: 4
• Total formula weight: 986699.80

Authors

Bashan, A.,Agmon, I.,Zarivatch, R.,Schluenzen, F.,Harms, J.M.,Berisio, R.,Bartels, H.,Hansen, H.A.,Yonath, A. (deposition date: 2003-01-02, release date: 2003-02-11, Last modification date: 2023-08-16)

Primary citation

Bashan, A.,Agmon, I.,Zarivatch, R.,Schluenzen, F.,Harms, J.M.,Berisio, R.,Bartels, H.,Franceschi, F.,Auerbach, T.,Hansen, H.A.,Kossoy, E.,Kessler, M.,Yonath, A.
Structural basis of the ribosomal machinery for Peptide bond formation, translocation, and nascent chain progression
Mol.Cell, 11:91-102, 2003

PubMed Abstract: Crystal structures of tRNA mimics complexed with the large ribosomal subunit of Deinococcus radiodurans indicate that remote interactions determine the precise orientation of tRNA in the peptidyl-transferase center (PTC). The PTC tolerates various orientations of puromycin derivatives and its flexibility allows the conformational rearrangements required for peptide-bond formation. Sparsomycin binds to A2602 and alters the PTC conformation. H69, the intersubunit-bridge connecting the PTC and decoding site, may also participate in tRNA placement and translocation. A spiral rotation of the 3' end of the A-site tRNA around a 2-fold axis of symmetry identified within the PTC suggests a unified ribosomal machinery for peptide-bond formation, A-to-P-site translocation, and entrance of nascent proteins into the exit tunnel. Similar 2-fold related regions, detected in all known structures of large ribosomal subunits, indicate the universality of this mechanism.

PubMed: 12535524
DOI: 10.1016/S1097-2765(03)00009-1

Experimental method

X-RAY DIFFRACTION (3.6 Å)