5Z00 image
Deposition Date 2017-12-17
Release Date 2018-05-02
Last Version Date 2024-03-27
Entry Detail
PDB ID:
5Z00
Keywords:
TRANSCRIPTION/DNA
Title:
AtVAL1 B3 domain in complex with 15bp-DNA
Biological Source:
Source Organism:
Arabidopsis thaliana (Taxon ID: 3702)
synthetic construct (Taxon ID: 32630)
Host Organism:
Arabidopsis thaliana
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.59 Å
R-Value Free:
0.26
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
P 1 21 1
5Z00 validation report
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*AP*AP*TP*TP*CP*TP*GP*CP*AP*TP*GP*GP*AP*TP*T)-3')
Chain IDs:A, D (auth: E), G (auth: I)
Chain Length:15
Number of Molecules:3
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*TP*AP*AP*TP*CP*CP*AP*TP*GP*CP*AP*GP*AP*AP*T)-3')
Chain IDs:B, H (auth: J)
Chain Length:15
Number of Molecules:2
Biological Source:synthetic construct
Protein Blast
Polymer Type:polypeptide(L)
Molecule:B3 domain-containing transcription repressor VAL1
Gene (Uniprot):VAL1
Chain IDs:C, F (auth: G), I (auth: K), J (auth: M)
Chain Length:128
Number of Molecules:4
Biological Source:Arabidopsis thaliana
UniProt ID:Q8W4L5 Pfam ID:PF02362
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*TP*AP*AP*TP*CP*CP*AP*TP*GP*CP*AP*GP*AP*AP*TP*T)-3')
Chain IDs:E (auth: F)
Chain Length:16
Number of Molecules:1
Biological Source:synthetic construct
Ligand Molecules
NA
Primary Citation
Structural insight into the role of VAL1 B3 domain for targeting to FLC locus in Arabidopsis thaliana.
Biochem. Biophys. Res. Commun. ? ? ? (2018)
PMID: 29733847 DOI: 10.1016/j.bbrc.2018.05.002

Abstact

Vernalization is a pivotal stage for some plants involving many epigenetic changes during cold exposure. In Arabidopsis, an essential step in vernalization for further flowering is successful silence the potent floral repressor Flowering Locus C (FLC) by repressing histone mark. AtVal1 is a multi-function protein containing five domains that participate into many recognition processes and is validated to recruit the repress histone modifier PHD-PRC2 complex and interact with components of the ASAP complex target to the FLC nucleation region through recognizing a cis element known as CME (cold memory element) by its plant-specific B3 domain. Here, we determine the crystal structure of the B3 domain in complex with Sph/RY motif in CME. Our structural analysis reveals the specific DNA recognition by B3 domain, combined with our in vitro experiments, we provide the structural insight into the important implication of AtVAL1-B3 domain in flowering process.

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Protein

Chemical

Disease

Primary Citation of related structures
5Z00