4p6f

Crystal structure of the peptolide 12C bound to bacterial ribosome

spinqualitylabelsall models 4p6f, resolution 3.60Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 4p6f is a 20 chain structure with sequence from Thermus thermophilus HB8. This structure supersedes the now removed PDB entries 4w2a, 4w2b, 4w2c and 4w2d. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 3.6Å Ligands: MG, PAR, T17, ZN Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function RS2_THET8 Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit.[HAMAP-Rule:MF_00291_B] Publication Abstract from PubMed Despite decades of research on the bacterial ribosome, the ribosomal exit tunnel is still poorly understood. Although it has been suggested that the exit tunnel is simply a convenient route of egress for the nascent chain, specific protein sequences serve to slow the rate of translation, suggesting some degree of interaction between the nascent peptide chain and the exit tunnel. To understand how the ribosome interacts with nascent peptide sequences, we synthesized and characterized a novel class of probe molecules. These peptide-macrolide (or "peptolide") conjugates were designed to present unique peptide sequences to the exit tunnel. Biochemical and X-ray structural analyses of the interactions between these probes and the ribosome reveal interesting insights about the exit tunnel. Using translation inhibition and RNA structure probing assays, we find the exit tunnel has a relaxed preference for the directionality (N --> C or C --> N orientation) of the nascent peptides. Moreover, the X-ray crystal structure of one peptolide derived from a positively charged, reverse Nuclear Localization Sequence peptide, bound to the 70S bacterial ribosome, reveals that the macrolide ring of the peptolide binds in the same position as other macrolides. However, the peptide tail folds over the macrolide ring, oriented toward the peptidyl transferase center and interacting in a novel manner with 23S rRNA residue C2442 and His69 of ribosomal protein L4. These data suggest that these peptolides are viable probes for interrogating nascent peptide-exit tunnel interaction. Macrolide-Peptide Conjugates as Probes of the Path of Travel of the Nascent Peptides through the Ribosome.,Washington AZ, Benicewicz DB, Canzoneri JC, Fagan CE, Mwakwari SC, Maehigashi T, Dunham CM, Oyelere AK ACS Chem Biol. 2014 Sep 22. PMID:25198768 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Transfer RNA (tRNA)

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