1MJI

DETAILED ANALYSIS OF RNA-PROTEIN INTERACTIONS WITHIN THE BACTERIAL RIBOSOMAL PROTEIN L5/5S RRNA COMPLEX

Summary for 1MJI

• Entry DOI: 10.2210/pdb1mji/pdb
• Descriptor: 5S rRNA fragment, 50S ribosomal protein L5, MAGNESIUM ION, ... (5 entities in total)
• Functional Keywords: ribosomal protein - 5s rrna complex, ribosome
• Biological source: Escherichia coli; More
• Total number of polymer chains: 4
• Total formula weight: 64181.28

Authors

Perederina, A.,Nevskaya, N.,Nikonov, O.,Nikulin, A.,Dumas, P.,Yao, M.,Tanaka, I.,Garber, M.,Gongadze, G.,Nikonov, S. (deposition date: 2002-08-28, release date: 2003-01-21, Last modification date: 2024-10-09)

Primary citation

Perederina, A.,Nevskaya, N.,Nikonov, O.,Nikulin, A.,Dumas, P.,Yao, M.,Tanaka, I.,Garber, M.,Gongadze, G.,Nikonov, S.
Detailed analysis of RNA-protein interactions within the bacterial ribosomal protein L5/5S rRNA complex
RNA, 8:1548-1557, 2002

PubMed Abstract: The crystal structure of ribosomal protein L5 from Thermus thermophilus complexed with a 34-nt fragment comprising helix III and loop C of Escherichia coli 5S rRNA has been determined at 2.5 A resolution. The protein specifically interacts with the bulged nucleotides at the top of loop C of 5S rRNA. The rRNA and protein contact surfaces are strongly stabilized by intramolecular interactions. Charged and polar atoms forming the network of conserved intermolecular hydrogen bonds are located in two narrow planar parallel layers belonging to the protein and rRNA, respectively. The regions, including these atoms conserved in Bacteria and Archaea, can be considered an RNA-protein recognition module. Comparison of the T. thermophilus L5 structure in the RNA-bound form with the isolated Bacillus stearothermophilus L5 structure shows that the RNA-recognition module on the protein surface does not undergo significant changes upon RNA binding. In the crystal of the complex, the protein interacts with another RNA molecule in the asymmetric unit through the beta-sheet concave surface. This protein/RNA interface simulates the interaction of L5 with 23S rRNA observed in the Haloarcula marismortui 50S ribosomal subunit.

PubMed: 12515387

Experimental method

X-RAY DIFFRACTION (2.5 Å)