1vy5 | pdb_00001vy5

Crystal structure of the Thermus thermophilus 70S ribosome in the post-catalysis state of peptide bond formation containing dipeptydil-tRNA in the A site and deacylated tRNA in the P site.

spinqualitylabelsall models 1vy5, resolution 2.55Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 1vy5 is a 20 chain structure with sequence from Escherichia coli, Thermus thermophilus HB8 and Synthetic construct. This structure supersedes the now removed PDB entries 4qcq, 4qcr, 4qcs and 4qct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2.55Å Ligands: 31M, 4SU, 5MC, 5MU, 7MG, K, MG, MIA, PSU, SF4, ZN Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function RS4_THET8 One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the body and platform of the 30S subunit. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01306_B] Publication Abstract from PubMed During peptide-bond formation on the ribosome, the alpha-amine of an aminoacyl-tRNA attacks the ester carbonyl carbon of a peptidyl-tRNA to yield a peptide lengthened by one amino acid. Although the ribosome's contribution to catalysis is predominantly entropic, the lack of high-resolution structural data for the complete active site in complex with full-length ligands has made it difficult to assess how the ribosome might influence the pathway of the reaction. Here, we present crystal structures of preattack and postcatalysis complexes of the Thermus thermophilus 70S ribosome at ~2.6-A resolution. These structures reveal a network of hydrogen bonds along which proton transfer could take place to ensure the concerted, rate-limiting formation of a tetrahedral intermediate. We propose that, unlike earlier models, the ribosome and the A-site tRNA facilitate the deprotonation of the nucleophile through the activation of a water molecule. A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome.,Polikanov YS, Steitz TA, Innis CA Nat Struct Mol Biol. 2014 Aug 17. doi: 10.1038/nsmb.2871. PMID:25132179 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Ribosomal protein THX 3D structures Ribosome 3D structures Transfer RNA (tRNA)

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