5DDZ

Crystal structure of the RTA-c10-P2 complex

Summary for 5DDZ

• Entry DOI: 10.2210/pdb5ddz/pdb
• Descriptor: Ricin, 60S acidic ribosomal protein P2 (3 entities in total)
• Functional Keywords: ricin, p2, complex, hydrolase-peptide complex, hydrolase/peptide
• Biological source: Ricinus communis (Castor bean); More
• Total number of polymer chains: 2
• Total formula weight: 32085.04

Authors

Zhu, Y.,Fan, X.,Wang, C.,Niu, L.,Li, X.,Teng, M. (deposition date: 2015-08-25, release date: 2016-09-07, Last modification date: 2023-11-08)

Primary citation

Fan, X.,Zhu, Y.,Wang, C.,Niu, L.,Teng, M.,Li, X.
Structural insights into the interaction of the ribosomal P stalk protein P2 with a type II ribosome-inactivating protein ricin
Sci Rep, 6:37803-37803, 2016

PubMed Abstract: Ricin is a type II ribosome-inactivating protein (RIP) that depurinates A at the sarcin-ricin loop of 28 S ribosomal RNA (rRNA), thus inactivating the ribosome by preventing elongation factors from binding to the GTPase activation centre. Recent studies have disclosed that the conserved C-terminal domain (CTD) of eukaryotic ribosomal P stalk proteins is involved in the process that RIPs target ribosome. However, the details of the molecular interaction between ricin and P stalk proteins remain unknown. Here, we report the structure of ricin-A chain (RTA) in a complex with the CTD of the human ribosomal protein P2. The structure shows that the Phe, Leu and Phe residues of P2 insert into a hydrophobic pocket formed by the Tyr, Arg, Phe and Ile residues of RTA, while Asp of P2 forms hydrogen bonds with Arg of RTA. The key residues in RTA and P2 for complex formation were mutated, and their importance was determined by pull-down assays. The results from cell-free translation assays further confirmed that the interaction with P stalk proteins is essential for the inhibition of protein synthesis by RTA. Taken together, our results provide a structural basis that will improve our understanding of the process by which ricin targets the ribosome, which will benefit the development of effective small-molecule inhibitors for use as therapeutic agents.

PubMed: 27886256
DOI: 10.1038/srep37803

Experimental method

X-RAY DIFFRACTION (1.5 Å)