6KYV

Crystal Structure of RIG-I and hairpin RNA with G-U wobble base pairs

Summary for 6KYV

• Entry DOI: 10.2210/pdb6kyv/pdb
• Descriptor: RNA (5'-R(*GP*GP*UP*AP*GP*AP*CP*GP*CP*UP*UP*CP*GP*GP*CP*GP*UP*UP*UP*GP*CP*C)-3'), Probable ATP-dependent RNA helicase DDX58, ZINC ION (3 entities in total)
• Functional Keywords: rig-i, ddx58, dsrna, wobble base pair, immune system
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 12
• Total formula weight: 512501.07

Authors

Kim, K.-H.,Hwang, J.,Kim, J.H.,Son, K.-P.,Jang, Y.,Kim, M.,Kang, S.-J.,Lee, J.-O.,Choi, B.-S. (deposition date: 2019-09-20, release date: 2020-09-23, Last modification date: 2023-11-22)

Primary citation

Kim, K.H.,Hwang, J.,Kim, J.H.,Son, K.P.,Jang, Y.,Kim, M.,Kang, S.J.,Lee, J.O.,Kang, J.Y.,Choi, B.S.
Structural and biophysical properties of RIG-I bound to dsRNA with G-U wobble base pairs.
Rna Biol., 17:325-334, 2020

PubMed Abstract: Retinoic acid-inducible gene I (RIG-I) is responsible for innate immunity via the recognition of short double-stranded RNAs in the cytosol. With the clue that G-U wobble base pairs in the influenza A virus's RNA promoter region are responsible for RIG-I activation, we determined the complex structure of RIG-I ΔCARD and a short hairpin RNA with G-U wobble base pairs by X-ray crystallography. Interestingly, the overall helical backbone trace was not affected by the presence of the wobble base pairs; however, the base pair inclination and helical axis angle changed upon RIG-I binding. NMR spectroscopy revealed that RIG-I binding renders the flexible base pair of the influenza A virus's RNA promoter region between the two G-U wobble base pairs even more flexible. Binding to RNA with wobble base pairs resulted in a more flexible RIG-I complex. This flexible complex formation correlates with the entropy-favoured binding of RIG-I and RNA, which results in tighter binding affinity and RIG-I activation. This study suggests that the structure and dynamics of RIG-I are tailored to the binding of specific RNA sequences with different flexibility.

PubMed: 31852354
DOI: 10.1080/15476286.2019.1700034

Experimental method

X-RAY DIFFRACTION (3 Å)