6FAS

Crystal structure of VAL1 B3 domain in complex with cognate DNA

Summary for 6FAS

• Entry DOI: 10.2210/pdb6fas/pdb
• Descriptor: B3 domain-containing transcription repressor VAL1, DNA (5'-D(*AP*GP*CP*CP*AP*TP*GP*CP*AP*CP*CP*G)-3'), DNA (5'-D(*CP*GP*GP*TP*GP*CP*AP*TP*GP*GP*CP*T)-3'), ... (4 entities in total)
• Functional Keywords: b3 dna binding domain, val1 transcriptional regulator, epigenome reader, complex, specific dna recognition, sph/ry sequence, dna binding protein
• Biological source: Arabidopsis thaliana (Mouse-ear cress); More
• Cellular location: Nucleus : Q8W4L5
• Total number of polymer chains: 6
• Total formula weight: 41448.39

Authors

Sasnauskas, G. (deposition date: 2017-12-17, release date: 2018-04-18, Last modification date: 2024-10-16)

Primary citation

Sasnauskas, G.,Kauneckaite, K.,Siksnys, V.
Structural basis of DNA target recognition by the B3 domain of Arabidopsis epigenome reader VAL1.
Nucleic Acids Res., 46:4316-4324, 2018

PubMed Abstract: Arabidopsis thaliana requires a prolonged period of cold exposure during winter to initiate flowering in a process termed vernalization. Exposure to cold induces epigenetic silencing of the FLOWERING LOCUS C (FLC) gene by Polycomb group (PcG) proteins. A key role in this epigenetic switch is played by transcriptional repressors VAL1 and VAL2, which specifically recognize Sph/RY DNA sequences within FLC via B3 DNA binding domains, and mediate recruitment of PcG silencing machinery. To understand the structural mechanism of site-specific DNA recognition by VAL1, we have solved the crystal structure of VAL1 B3 domain (VAL1-B3) bound to a 12 bp oligoduplex containing the canonical Sph/RY DNA sequence 5'-CATGCA-3'/5'-TGCATG-3'. We find that VAL1-B3 makes H-bonds and van der Waals contacts to DNA bases of all six positions of the canonical Sph/RY element. In agreement with the structure, in vitro DNA binding studies show that VAL1-B3 does not tolerate substitutions at any position of the 5'-TGCATG-3' sequence. The VAL1-B3-DNA structure presented here provides a structural model for understanding the specificity of plant B3 domains interacting with the Sph/RY and other DNA sequences.

PubMed: 29660015
DOI: 10.1093/nar/gky256

Experimental method

X-RAY DIFFRACTION (1.9 Å)