6R0M

Histone fold domain of AtNF-YB2/NF-YC3 in P212121

Summary for 6R0M

• Entry DOI: 10.2210/pdb6r0m/pdb
• Descriptor: NF-YB2, NF-YC3 (3 entities in total)
• Functional Keywords: nf-y, transcription factor, arabidopsis, transcription
• Biological source: Arabidopsis thaliana (thale cress); More
• Total number of polymer chains: 4
• Total formula weight: 44575.48

Authors

Chaves-Sanjuan, A.,Gnesutta, N.,Chiara, M.,Bernardini, A.,Fornara, F.,Horner, D.,Nardini, M.,Mantovani, R. (deposition date: 2019-03-13, release date: 2020-09-30, Last modification date: 2024-01-24)

Primary citation

Chaves-Sanjuan, A.,Gnesutta, N.,Gobbini, A.,Martignago, D.,Bernardini, A.,Fornara, F.,Mantovani, R.,Nardini, M.
Structural determinants for NF-Y subunit organization and NF-Y/DNA association in plants.
Plant J., 105:49-61, 2021

PubMed Abstract: NF-Y transcription factor comprises three subunits: NF-YA, NF-YB and NF-YC. NF-YB and NF-YC dimerize through their histone fold domain (HFD), which can bind DNA in a non-sequence-specific fashion while serving as a scaffold for NF-YA trimerization. Upon trimerization, NF-YA specifically recognizes the CCAAT box sequence on promoters and enhancers. In plants, each NF-Y subunit is encoded by several genes giving rise to hundreds of potential heterotrimeric combinations. In addition, plant NF-YBs and NF-YCs interact with other protein partners to recognize a plethora of genomic motifs, as the CCT protein family that binds CORE sites. The NF-Y subunit organization and its DNA-binding properties, together with the NF-Y HFD capacity to adapt different protein modules, represent plant-specific features that play a key role in development, growth and reproduction. Despite their relevance, these features are still poorly understood at the molecular level. Here, we present the structures of Arabidopsis and rice NF-YB/NF-YC dimers, and of an Arabidopsis NF-Y trimer in complex with the FT CCAAT box, together with biochemical data on NF-Y mutants. The dimeric structures identify the key residues for NF-Y HFD stabilization. The NF-Y/DNA structure and the mutation experiments shed light on HFD trimerization interface properties and the NF-YA sequence appetite for the bases flanking the CCAAT motif. These data explain the logic of plant NF-Y gene expansion: the trimerization adaptability and the flexible DNA-binding rules serve the scopes of accommodating the large number of NF-YAs, CCTs and possibly other NF-Y HFD binding partners and a diverse audience of genomic motifs.

PubMed: 33098724
DOI: 10.1111/tpj.15038

Experimental method

X-RAY DIFFRACTION (2.3 Å)