4V5K

Structure of cytotoxic domain of colicin E3 bound to the 70S ribosome

This is a non-PDB format compatible entry.

Summary for 4V5K

• Entry DOI: 10.2210/pdb4v5k/pdb
• Related: 1DV4 1E44 1EG0 1EMI 1FJG 1FKA 1G1X 1GIX 1HNW 1HNX 1HNZ 1HR0 1I94 1I95 1I96 1I97 1IBK 1IBL 1IBM 1J5E 1JCH 1JGO 1JGP 1JGQ 1L1U 1N32 1N33 1N34 1N36 1PN7 1PN8 1PNS 1PNX 1QD7 1QZC 1RSS 1TWT 1UJW 1VOV 1XMO 1XMQ 1XNQ 1XNR 1YL4 2B64 2B9M 2B9O 2F4V 2J00 2J02 2JL5 2JL7 2UU9 2UUA 2UUB 2UUC 2UXB 2UXC 2UXD 2V46 2V48 2VQE 2VQF 2WDG 2WDH 2WDK 2WDM 2WH1 2WH3 2WRN 2WRQ 2X9R 2X9T
• Descriptor: 16S ribosomal RNA, 30S RIBOSOMAL PROTEIN S10, 30S RIBOSOMAL PROTEIN S11, ... (61 entities in total)
• Functional Keywords: ribosome
• Biological source: Escherichia coli K-12; More
• Total number of polymer chains: 116
• Total formula weight: 4561558.57

Authors

Ng, C.L.,Lang, K.,Meenan, N.A.G.,Sharma, A.,Kelley, A.C.,Kleanthous, C.,Ramakrishnan, V. (deposition date: 2010-05-29, release date: 2014-07-09, Last modification date: 2024-11-13)

Primary citation

Ng, C.L.,Lang, K.,Meenan, N.A.G.,Sharma, A.,Kelley, A.C.,Kleanthous, C.,Ramakrishnan, V.
Structural Basis for 16S Ribosomal RNA Cleavage by the Cytotoxic Domain of Colicin E3.
Nat.Struct.Mol.Biol., 17:1241-1246, 2010

PubMed Abstract: The toxin colicin E3 targets the 30S subunit of bacterial ribosomes and cleaves a phosphodiester bond in the decoding center. We present the crystal structure of the 70S ribosome in complex with the cytotoxic domain of colicin E3 (E3-rRNase). The structure reveals how the rRNase domain of colicin binds to the A site of the decoding center in the 70S ribosome and cleaves the 16S ribosomal RNA (rRNA) between A1493 and G1494. The cleavage mechanism involves the concerted action of conserved residues Glu62 and His58 of the cytotoxic domain of colicin E3. These residues activate the 16S rRNA for 2' OH-induced hydrolysis. Conformational changes observed for E3-rRNase, 16S rRNA and helix 69 of 23S rRNA suggest that a dynamic binding platform is required for colicin E3 binding and function.

PubMed: 20852642
DOI: 10.1038/nsmb.1896

Experimental method

X-RAY DIFFRACTION (3.2 Å)