9LRI

Crystal Structure of Thermus thermophilus KhpB/EloR complexed with RNA

Summary for 9LRI

• Entry DOI: 10.2210/pdb9lri/pdb
• Descriptor: Probable DNA/RNA-binding protein (Jag-related protein), RNA (5'-R(P*CP*CP*CP*CP*CP*CP*C)-3'), CYTIDINE-5'-MONOPHOSPHATE, ... (4 entities in total)
• Functional Keywords: rna-binding protein, kh domain, r3h domain, thermus thermophilus, rna binding protein, rna binding protein-rna complex, rna binding protein/rna
• Biological source: Thermus thermophilus HB8; More
• Total number of polymer chains: 3
• Total formula weight: 45418.27

Authors

Fukui, K.,Murakawa, T.,Yano, T. (deposition date: 2025-01-31, release date: 2025-07-23, Last modification date: 2025-09-17)

Primary citation

Fukui, K.,Murakawa, T.,Baba, S.,Kumasaka, T.,Yano, T.
KH-R3H domain cooperation in RNA recognition by the global RNA-binding protein KhpB.
Nat Commun, 16:8028-8028, 2025

PubMed Abstract: KhpB, also known as EloR, is a recently discovered global RNA-binding protein in various pathogenic bacteria that regulates critical cellular processes. KhpB is unique in containing both an R3H domain and a KH domain, which are universal RNA/DNA-binding domains found across various proteins involved in diverse cellular functions. However, the precise roles of these domains in KhpB's RNA-binding mechanism remain unclear, particularly as no structural data of the R3H domain bound to RNA/DNA have been reported for any protein. In this study, we present the crystal structures of both the RNA-free and RNA-bound forms of Thermus thermophilus KhpB dimer. These structures reveal that the KH and R3H domains cooperate to form a composite RNA-binding site capable of binding a single RNA molecule. Notably, the coordinated interaction requires RNA molecules that are at least 7 nucleotides long. This interaction induces conformational changes, including the closure of the RNA-binding cleft between the two domains. The structural data further reveal that KhpB primarily interacts with the phosphate backbone of RNA, while most of the base moieties remain solvent-exposed. These findings provide structural insights into the molecular function of KhpB and shed light on the RNA-binding strategies of other R3H domain-containing proteins.

PubMed: 40903470
DOI: 10.1038/s41467-025-62302-y

Experimental method

X-RAY DIFFRACTION (2.65 Å)