5Z00

AtVAL1 B3 domain in complex with 15bp-DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.587 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural insight into the role of VAL1 B3 domain for targeting to FLC locus in Arabidopsis thaliana.

Wu, B.X.Zhang, M.M.Su, S.C.Liu, H.H.Gan, J.H.Ma, J.B.

(2018) Biochem. Biophys. Res. Commun. --: --

  • DOI: 10.1016/j.bbrc.2018.05.002
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 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 ...

    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.


    Organizational Affiliation

    State Key Laboratory of Genetic Engineering, Collaborative Innovation Centre of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China. Electronic address: bxwu15@fudan.edu.cn.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
B3 domain-containing transcription repressor VAL1
C, G, K, M
128Arabidopsis thalianaMutation(s): 0 
Gene Names: VAL1 (HSI2)
Find proteins for Q8W4L5 (Arabidopsis thaliana)
Go to UniProtKB:  Q8W4L5
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*AP*TP*TP*CP*TP*GP*CP*AP*TP*GP*GP*AP*TP*T)-3')A,E,I15synthetic construct
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*AP*AP*TP*CP*CP*AP*TP*GP*CP*AP*GP*AP*AP*T)-3')B,J15synthetic construct
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*AP*AP*TP*CP*CP*AP*TP*GP*CP*AP*GP*AP*AP*TP*T)-3')F16synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.587 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.216 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 68.223α = 90.00
b = 97.416β = 110.19
c = 71.149γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-12-17 
  • Released Date: 2018-05-02 
  • Deposition Author(s): Wu, B.X., Zhang, M.M.

Revision History 

  • Version 1.0: 2018-05-02
    Type: Initial release
  • Version 1.1: 2018-05-30
    Type: Data collection, Database references