6FAS

Crystal structure of VAL1 B3 domain in complex with cognate DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structural basis of DNA target recognition by the B3 domain of Arabidopsis epigenome reader VAL1.

Sasnauskas, G., Kauneckaite, K., Siksnys, V.

(2018) Nucleic Acids Res 46: 4316-4324

  • DOI: https://doi.org/10.1093/nar/gky256
  • Primary Citation of Related Structures:  
    6FAS

  • PubMed Abstract: 

    • Arabidopsis thaliana requires a prolonged period of cold exposure during winter to initiate flowering in a process termed vernalization. Exposure to cold induces epigenetic silencing of the FLOWERING LOCUS C (FLC) gene by Polycomb group (PcG) proteins. A key role in this epigenetic switch is played by transcriptional repressors VAL1 and VAL2, which specifically recognize Sph/RY DNA sequences within FLC via B3 DNA binding domains, and mediate recruitment of PcG silencing machinery ...

    Arabidopsis thaliana requires a prolonged period of cold exposure during winter to initiate flowering in a process termed vernalization. Exposure to cold induces epigenetic silencing of the FLOWERING LOCUS C (FLC) gene by Polycomb group (PcG) proteins. A key role in this epigenetic switch is played by transcriptional repressors VAL1 and VAL2, which specifically recognize Sph/RY DNA sequences within FLC via B3 DNA binding domains, and mediate recruitment of PcG silencing machinery. To understand the structural mechanism of site-specific DNA recognition by VAL1, we have solved the crystal structure of VAL1 B3 domain (VAL1-B3) bound to a 12 bp oligoduplex containing the canonical Sph/RY DNA sequence 5'-CATGCA-3'/5'-TGCATG-3'. We find that VAL1-B3 makes H-bonds and van der Waals contacts to DNA bases of all six positions of the canonical Sph/RY element. In agreement with the structure, in vitro DNA binding studies show that VAL1-B3 does not tolerate substitutions at any position of the 5'-TGCATG-3' sequence. The VAL1-B3-DNA structure presented here provides a structural model for understanding the specificity of plant B3 domains interacting with the Sph/RY and other DNA sequences.

    Organizational Affiliation: 

    Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
B3 domain-containing transcription repressor VAL1
A, B
119Arabidopsis thalianaMutation(s): 0 
Gene Names: VAL1, HSI2, At2g30470, T6B20.17
UniProt
Find proteins for Q8W4L5 (Arabidopsis thaliana)
Explore Q8W4L5 
Go to UniProtKB:  Q8W4L5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8W4L5
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*AP*GP*CP*CP*AP*TP*GP*CP*AP*CP*CP*G)-3')
C, E
12synthetic construct
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(*CP*GP*GP*TP*GP*CP*AP*TP*GP*GP*CP*T)-3')
D, F
12synthetic construct
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME
A, B
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.091α = 90
b = 86.577β = 94.14
c = 65.16γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Research Council of LithuaniaLithuaniaMIP-106/2015

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-18
    Type: Initial release
  • Version 1.1: 2018-04-25
    Changes: Data collection, Database references
  • Version 1.2: 2018-05-16
    Changes: Data collection, Database references