7VP3

Structure of a transcription factor and DNA complex

Summary for 7VP3

• Entry DOI: 10.2210/pdb7vp3/pdb
• Descriptor: DNA (5'-D(*TP*GP*GP*GP*GP*AP*CP*CP*CP*AP*C)-3'), Transcription factor TCP15, DNA (5'-D(*AP*TP*GP*TP*GP*GP*GP*TP*CP*CP*CP*C)-3') (3 entities in total)
• Functional Keywords: complex, transcription factor, transcription, dna binding protein
• Biological source: Arabidopsis thaliana (thale cress); More
• Total number of polymer chains: 16
• Total formula weight: 94581.83

Authors

Zhang, Y.,Xu, Y.P.,Wang, B.,Su, X.D. (deposition date: 2021-10-15, release date: 2022-10-19, Last modification date: 2026-02-11)

Primary citation

Zhang, Y.,Xu, Y.P.,Nie, J.K.,Chen, H.,Qin, G.,Wang, B.,Su, X.D.
DNA-TCP complex structures reveal a unique recognition mechanism for TCP transcription factor families.
Nucleic Acids Res., 51:434-448, 2023

PubMed Abstract: Plant-specific TCP transcription factors are key regulators of diverse plant functions. TCP transcription factors have long been annotated as basic helix-loop-helix (bHLH) transcription factors according to remote sequence homology without experimental validation, and their consensus DNA-binding sequences and protein-DNA recognition mechanisms have remained elusive. Here, we report the crystal structures of the class I TCP domain from AtTCP15 and the class II TCP domain from AtTCP10 in complex with different double-stranded DNA (dsDNA). The complex structures reveal that the TCP domain is a distinct DNA-binding motif and the homodimeric TCP domains adopt a unique three-site recognition mode, binding to dsDNA mainly through a central pair of β-strands formed by the dimer interface and two basic flexible loops from each monomer. The consensus DNA-binding sequence for class I TCPs is a perfectly palindromic 11 bp (GTGGGNCCCAC), whereas that for class II TCPs is a near-palindromic 11 bp (GTGGTCCCCAC). The unique DNA binding mode allows the TCP domains to display broad specificity for a range of DNA sequences even shorter than 11 bp, adding further complexity to the regulatory network of plant TCP transcription factors.

PubMed: 36546761
DOI: 10.1093/nar/gkac1171

Experimental method

X-RAY DIFFRACTION (3.003 Å)