6A57

Structure of histone demethylase REF6 complexed with DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 6A58 6A59


Literature

Crystal structures of REF6 and its complex with DNA reveal diverse recognition mechanisms.

Tian, Z.Li, X.Li, M.Wu, W.Zhang, M.Tang, C.Li, Z.Liu, Y.Chen, Z.Yang, M.Ma, L.Caba, C.Tong, Y.Lam, H.M.Dai, S.Chen, Z.

(2020) Cell Discov 6: 17-17

  • DOI: https://doi.org/10.1038/s41421-020-0150-6
  • Primary Citation of Related Structures:  
    6A57, 6A58, 6A59

  • PubMed Abstract: 

    Relative of Early Flowing 6 (REF6) is a DNA-sequence-specific H3K27me3/2 demethylase that contains four zinc finger (ZnF) domains and targets several thousand genes in Arabidopsis thaliana . The ZnF domains are essential for binding target genes, but the structural basis remains unclear. Here, we determined crystal structures of the ZnF domains and REF6-DNA complex, revealing a unique REF6-family-specific half-cross-braced ZnF (RCZ) domain and two C2H2-type ZnFs. DNA-binding induces a profound conformational change in the hinge region of REF6. Each REF6 recognizes six bases and DNA methylation reduces the binding affinity. Both the acidic region and basic region are important for the self-association of REF6. The REF6 DNA-binding affinity is determined by the sequence-dependent conformations of DNA and also the cooperativity in different target motifs. The conformational plasticity enables REF6 to function as a global transcriptional regulator that directly binds to many diverse genes, revealing the structural basis for the epigenetic modification recognition.


  • Organizational Affiliation

    1State Key Laboratory of Agrobiotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, 100193 Beijing, China.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysine-specific demethylase REF6140Arabidopsis thalianaMutation(s): 0 
Gene Names: REF6JMJ12PKDM9AAt3g48430T29H11_50
EC: 1.14.11
UniProt
Find proteins for Q9STM3 (Arabidopsis thaliana)
Explore Q9STM3 
Go to UniProtKB:  Q9STM3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9STM3
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*TP*TP*TP*CP*TP*CP*TP*GP*TP*TP*TP*TP*GP*TP*C)-3')16Arabidopsis thaliana
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*GP*AP*CP*AP*AP*AP*AP*CP*AP*GP*AP*GP*AP*AP*A)-3')16Arabidopsis thaliana
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.087α = 90
b = 96.087β = 90
c = 73.905γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
HKL2Mapphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Basic Research Program of China (973 Program)China2016YFC1200400

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2020-07-08
    Changes: Author supporting evidence, Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references