7W27

Crystal structure of BEND3-BEN4-DNA complex

Summary for 7W27

• Entry DOI: 10.2210/pdb7w27/pdb
• Descriptor: DNA (5'-D(P*GP*GP*AP*CP*CP*CP*AP*CP*GP*CP*AP*GP*C)-3'), DNA (5'-D(P*GP*GP*CP*TP*GP*CP*GP*TP*GP*GP*GP*TP*C)-3'), BEN domain-containing protein 3, ... (4 entities in total)
• Functional Keywords: protein-dna interactions, dna binding protein-dna complex, dna binding protein/dna
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 3
• Total formula weight: 21182.42

Authors

Zheng, L.,Ren, A. (deposition date: 2021-11-22, release date: 2022-02-23, Last modification date: 2024-10-09)

Primary citation

Zheng, L.,Liu, J.,Niu, L.,Kamran, M.,Yang, A.W.H.,Jolma, A.,Dai, Q.,Hughes, T.R.,Patel, D.J.,Zhang, L.,Prasanth, S.G.,Yu, Y.,Ren, A.,Lai, E.C.
Distinct structural bases for sequence-specific DNA binding by mammalian BEN domain proteins.
Genes Dev., 36:225-240, 2022

PubMed Abstract: The BEN domain is a recently recognized DNA binding module that is present in diverse metazoans and certain viruses. Several BEN domain factors are known as transcriptional repressors, but, overall, relatively little is known of how BEN factors identify their targets in humans. In particular, X-ray structures of BEN domain:DNA complexes are only known for factors bearing a single BEN domain, which lack direct vertebrate orthologs. Here, we characterize several mammalian BEN domain (BD) factors, including from two NACC family BTB-BEN proteins and from BEND3, which has four BDs. In vitro selection data revealed sequence-specific binding activities of isolated BEN domains from all of these factors. We conducted detailed functional, genomic, and structural studies of BEND3. We show that BD4 is a major determinant for in vivo association and repression of endogenous BEND3 targets. We obtained a high-resolution structure of BEND3-BD4 bound to its preferred binding site, which reveals how BEND3 identifies cognate DNA targets and shows differences with one of its non-DNA-binding BEN domains (BD1). Finally, comparison with our previous invertebrate BEN structures, along with additional structural predictions using AlphaFold2 and RoseTTAFold, reveal distinct strategies for target DNA recognition by different types of BEN domain proteins. Together, these studies expand the DNA recognition activities of BEN factors and provide structural insights into sequence-specific DNA binding by mammalian BEN proteins.

PubMed: 35144965
DOI: 10.1101/gad.348993.121

Experimental method

X-RAY DIFFRACTION (1.49 Å)