9LNJ
Crystal structure of VANC21 in complex with its target DNA (5-bromouridine substituted).
Summary for 9LNJ
| Entry DOI | 10.2210/pdb9lnj/pdb |
| Descriptor | VANC21, VANC21 binding DNA fragment (motif strand), VANC21 binding DNA fragment (complementary strand), ... (5 entities in total) |
| Functional Keywords | protein-dna complex, transposon, vandal, dna binding protein, dna binding protein-dna complex, dna binding protein/dna |
| Biological source | Arabidopsis thaliana (thale cress) More |
| Total number of polymer chains | 3 |
| Total formula weight | 52418.21 |
| Authors | Tanaka, Y.,Shihoya, W.,Hirano, H.,Itoh, Y.,Kakutani, T.,Nureki, O. (deposition date: 2025-01-21, release date: 2025-12-10, Last modification date: 2026-02-18) |
| Primary citation | Tanaka, Y.,Osakabe, A.,Shihoya, W.,Hirano, H.,Itoh, Y.,Kakutani, T.,Nureki, O. Structure and evolution of the sequence-specific anti-silencing factor VANC21 and its target DNA. Genes Genet Syst, 101:-, 2026 Cited by PubMed Abstract: VANDAL family transposons are DNA transposons prevalent in Arabidopsis and related plants. A notable feature of VANDAL is that they can overcome epigenetic silencing from the host, using a VANC protein encoded in each VANDAL members: VANC21 protein encoded in VANDAL21 specifically accumulates on its target DNA motifs condensed in the non-coding regions of this TE and induces loss of DNA methylation, transcriptional derepression, and mobilization of them. In this study, to elucidate the mechanism of how VANC subtypes have diverged to bind specifically to their own target motifs in their cognate VANDAL subfamilies, we determined the crystal structure of VANC21 in complex with its target DNA at 2.0 Å resolution. The VANC structure adopts a globular novel fold with a Zn ion coordinated at the DNA-binding site. Interestingly, most DNA-interacting VANC residues are located in the loops but not in the conserved regions among VANC subtypes. This observation suggests that the high variability of DNA-interacting regions of VANC proteins brought about the co-evolution of VANCs and their target sequences. This rapid differentiation by co-evolution enabled VANDAL family TEs to proliferate while avoiding deleterious effects on the host fitness. Therefore, our findings help understand the adaptive evolutionary strategy for the survival of parasitic sequences. PubMed: 41260640DOI: 10.1266/ggs.25-00096 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2 Å) |
Structure validation
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