5YZY | pdb_00005yzy

AtVAL1 B3 domain in complex with 13bp-DNA

• PDB DOI: https://doi.org/10.2210/pdb5YZY/pdb
• NAKB: 5YZY

• Classification: TRANSCRIPTION/DNA
• Organism(s): synthetic construct, Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 
  0.257 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

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 

• PubMed: 29733847 
• DOI: https://doi.org/10.1016/j.bbrc.2018.05.002
• Primary Citation Related Structures: 
  5YZY, 5YZZ, 5Z00


• 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) 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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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: [e-mail].
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.
State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai, 200438, China.
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: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 22.34 kDa 
• Atom Count: 1,394 
• Modeled Residue Count: 137 
• Deposited Residue Count: 154 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
B3 domain-containing transcription repressor VAL1	C	128	Arabidopsis thaliana	Mutation(s): 0  Gene Names: VAL1, HSI2, At2g30470, T6B20.17
UniProt
Find proteins for Q8W4L5 (Arabidopsis thaliana) Explore Q8W4L5  Go to UniProtKB:  Q8W4L5

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*TP*TP*CP*TP*GP*CP*AP*TP*GP*GP*AP*T)-3')	A	13	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*AP*TP*CP*CP*AP*TP*GP*CP*AP*GP*AP*A)-3')	B	13	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HG	D [auth C]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free:  0.257 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.78	α = 90
b = 87.78	β = 90
c = 148.735	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELXDE	phasing

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Data collection, Database references
• Version 1.2: 2024-03-27
  Changes: Data collection, Database references