6LQE

Crystal structure of Arabidopsis ARID5 PHD finger in complex with H3K4me3 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Dual Recognition of H3K4me3 and DNA by the ISWI Component ARID5 Regulates the Floral Transition in Arabidopsis.

Tan, L.M.Liu, R.Gu, B.W.Zhang, C.J.Luo, J.Guo, J.Wang, Y.Chen, L.Du, X.Li, S.Shao, C.R.Su, Y.N.Cai, X.W.Lin, R.N.Li, L.Chen, S.Du, J.He, X.J.

(2020) Plant Cell 32: 2178-2195

  • DOI: https://doi.org/10.1105/tpc.19.00944
  • Primary Citation of Related Structures:  
    6LQE, 6LQF

  • PubMed Abstract: 

    Chromatin remodeling and histone modifications are important for development and floral transition in plants. However, it is largely unknown whether and how these two epigenetic regulators coordinately regulate the important biological processes. Here, we identified three types of Imitation Switch (ISWI) chromatin-remodeling complexes in Arabidopsis ( Arabidopsis thaliana ). We found that AT-RICH INTERACTING DOMAIN5 (ARID5), a subunit of a plant-specific ISWI complex, can regulate development and floral transition. The ARID-PHD dual domain cassette of ARID5 recognizes both the H3K4me3 histone mark and AT-rich DNA. We determined the ternary complex structure of the ARID5 ARID-PHD cassette with an H3K4me3 peptide and an AT-containing DNA. The H3K4me3 peptide is combinatorially recognized by the PHD and ARID domains, while the DNA is specifically recognized by the ARID domain. Both PHD and ARID domains are necessary for the association of ARID5 with chromatin. The results suggest that the dual recognition of AT-rich DNA and H3K4me3 by the ARID5 ARID-PHD cassette may facilitate the association of the ISWI complex with specific chromatin regions to regulate development and floral transition.


  • Organizational Affiliation

    National Institute of Biological Sciences, Beijing 102206, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AT-rich interactive domain-containing protein 476Arabidopsis thalianaMutation(s): 0 
Gene Names: ARID4At3g43240F7K15.90
UniProt
Find proteins for Q6NQ79 (Arabidopsis thaliana)
Explore Q6NQ79 
Go to UniProtKB:  Q6NQ79
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6NQ79
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
15-mer peptide from Histone H3.2B [auth P]15Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P59226 (Arabidopsis thaliana)
Explore P59226 
Go to UniProtKB:  P59226
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP59226
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
M3L
Query on M3L
B [auth P]L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 27.922α = 90
b = 27.922β = 90
c = 124.513γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2020-06-03 
  • Deposition Author(s): Liu, R., Du, J.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31622032

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-03
    Type: Initial release
  • Version 1.1: 2020-08-19
    Changes: Database references, Derived calculations