4W2H

Crystal structure of the Thermus thermophilus 70S ribosome in complex with pactamycin (co-crystallized), mRNA and deacylated tRNA in the P site

This is a non-PDB format compatible entry.

Summary for 4W2H

• Entry DOI: 10.2210/pdb4w2h/pdb
• Descriptor: 16S Ribosomal RNA, 30S Ribosomal Protein S10, 30S Ribosomal Protein S11, ... (61 entities in total)
• Functional Keywords: pactamycin, antibiotic, 70s ribosome, inhibition of translation, initiation inhibitor, 30s subunit with pactamycin (co-crystallized), mrna, deacylated p-site trna, and e-site trna acceptor stem of the 1st 70s ribosome in the asu, functional complex of bacterial 70s ribosome with antibiotic pactamycin (extended conformation), 50s subunit of the 1st 70s ribosome in the asu, ribosome-antibiotic complex, ribosome/antibiotic
• Biological source: Escherichia coli; More
• Total number of polymer chains: 110
• Total formula weight: 4503125.04

Authors

Polikanov, Y.S.,Osterman, I.A.,Szal, T.,Tashlitsky, V.N.,Serebryakova, M.V.,Kusochek, P.,Bulkley, D.,Malanicheva, I.A.,Efimenko, T.A.,Efremenkova, O.V.,Konevega, A.L.,Shaw, K.J.,Bogdanov, A.A.,Rodnina, M.V.,Dontsova, O.A.,Mankin, A.S.,Steitz, T.A.,Sergiev, P.V. (deposition date: 2014-09-12, release date: 2014-10-15, Last modification date: 2024-10-16)

Primary citation

Polikanov, Y.S.,Osterman, I.A.,Szal, T.,Tashlitsky, V.N.,Serebryakova, M.V.,Kusochek, P.,Bulkley, D.,Malanicheva, I.A.,Efimenko, T.A.,Efremenkova, O.V.,Konevega, A.L.,Shaw, K.J.,Bogdanov, A.A.,Rodnina, M.V.,Dontsova, O.A.,Mankin, A.S.,Steitz, T.A.,Sergiev, P.V.
Amicoumacin a inhibits translation by stabilizing mRNA interaction with the ribosome.
Mol.Cell, 56:531-540, 2014

PubMed Abstract: We demonstrate that the antibiotic amicoumacin A (AMI) is a potent inhibitor of protein synthesis. Resistance mutations in helix 24 of the 16S rRNA mapped the AMI binding site to the small ribosomal subunit. The crystal structure of bacterial ribosome in complex with AMI solved at 2.4 Å resolution revealed that the antibiotic makes contacts with universally conserved nucleotides of 16S rRNA in the E site and the mRNA backbone. Simultaneous interactions of AMI with 16S rRNA and mRNA and the in vivo experimental evidence suggest that it may inhibit the progression of the ribosome along mRNA. Consistent with this proposal, binding of AMI interferes with translocation in vitro. The inhibitory action of AMI can be partly compensated by mutations in the translation elongation factor G.

PubMed: 25306919
DOI: 10.1016/j.molcel.2014.09.020

Experimental method

X-RAY DIFFRACTION (2.7 Å)