6JNM

REF6 ZnF2-4-NAC004-mC3 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

DNA methylation repels targeting of Arabidopsis REF6.

Qiu, Q.Mei, H.Deng, X.He, K.Wu, B.Yao, Q.Zhang, J.Lu, F.Ma, J.Cao, X.

(2019) Nat Commun 10: 2063-2063

  • DOI: 10.1038/s41467-019-10026-1
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • RELATIVE OF EARLY FLOWERING 6 (REF6/JMJ12), a Jumonji C (JmjC)-domain-containing H3K27me3 histone demethylase, finds its target loci in Arabidopsis genome by directly recognizing the CTCTGYTY motif via its zinc-finger (ZnF) domains. REF6 tends to bin ...

    RELATIVE OF EARLY FLOWERING 6 (REF6/JMJ12), a Jumonji C (JmjC)-domain-containing H3K27me3 histone demethylase, finds its target loci in Arabidopsis genome by directly recognizing the CTCTGYTY motif via its zinc-finger (ZnF) domains. REF6 tends to bind motifs located in active chromatin states that are depleted for heterochromatic modifications. However, the underlying mechanism remains unknown. Here, we show that REF6 preferentially bind to hypo-methylated CTCTGYTY motifs in vivo, and that CHG methylation decreases REF6 DNA binding affinity in vitro. In addition, crystal structures of ZnF-clusters in complex with DNA oligonucleotides reveal that 5-methylcytosine is unfavorable for REF6 binding. In drm1 drm2 cmt2 cmt3 (ddcc) quadruple mutants, in which non-CG methylation is significantly reduced, REF6 can ectopically bind a small number of new target loci, most of which are located in or neighbored with short TEs in euchromatic regions. Collectively, our findings reveal that DNA methylation, likely acting in combination with other epigenetic modifications, may partially explain why REF6 binding is depleted in heterochromatic loci.


    Organizational Affiliation

    Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Beijing, 100101, China. xfcao@genetics.ac.cn.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysine-specific demethylase REF6A, B101Arabidopsis thalianaMutation(s): 0 
Gene Names: REF6JMJ12PKDM9AAt3g48430T29H11_50
EC: 1.14.11
Find proteins for Q9STM3 (Arabidopsis thaliana)
Explore Q9STM3 
Go to UniProtKB:  Q9STM3
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*TP*CP*TP*(5CM)P*TP*GP*TP*TP*TP*TP*G)-3')D, F12synthetic construct
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*AP*AP*AP*AP*CP*AP*GP*AP*GP*AP*A)-3')C, E12synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.516α = 90
b = 88.516β = 90
c = 72.33γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-03-27
    Type: Initial release
  • Version 1.1: 2019-05-15
    Changes: Data collection, Database references