6LMR

Solution structure of cold shock domain and ssDNA complex

Summary for 6LMR

• Entry DOI: 10.2210/pdb6lmr/pdb
• Descriptor: Y-box-binding protein 1, DNA (5'-D(P*AP*AP*CP*AP*CP*CP*T)-3') (2 entities in total)
• Functional Keywords: y-box, cold shock domain, ssnda, complex, dna binding protein
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 2
• Total formula weight: 13879.49

Authors

Fan, J.,Yang, D. (deposition date: 2019-12-26, release date: 2020-07-22, Last modification date: 2024-05-15)

Primary citation

Zhang, J.,Fan, J.S.,Li, S.,Yang, Y.,Sun, P.,Zhu, Q.,Wang, J.,Jiang, B.,Yang, D.,Liu, M.
Structural basis of DNA binding to human YB-1 cold shock domain regulated by phosphorylation.
Nucleic Acids Res., 48:9361-9371, 2020

PubMed Abstract: Human Y-box binding protein 1 (YB-1) is a multifunctional protein and overexpressed in many types of cancer. It specifically recognizes DNA/RNA through a cold shock domain (CSD) and regulates nucleic acid metabolism. The C-terminal extension of CSD and the phosphorylation of S102 are indispensable for YB-1 function. Until now, the roles of the C-terminal extension and phosphorylation in gene transcription and translation are still largely unknown. Here, we solved the structure of human YB-1 CSD with a C-terminal extension sequence (CSDex). The structure reveals that the extension interacts with several residues in the conventional CSD and adopts a rigid structure instead of being disordered. Either deletion of this extension or phosphorylation of S102 destabilizes the protein and results in partial unfolding. Structural characterization of CSDex in complex with a ssDNA heptamer shows that all the seven nucleotides are involved in DNA-protein interactions and the C-terminal extension provides a unique DNA binding site. Our DNA-binding study indicates that CSDex can recognize more DNA sequences than previously thought and the phosphorylation reduces its binding to ssDNA dramatically. Our results suggest that gene transcription and translation can be regulated by changing the affinity of CSDex binding to DNA and RNA through phosphorylation, respectively.

PubMed: 32710623
DOI: 10.1093/nar/gkaa619

Experimental method

SOLUTION NMR