6LQF

Crystal structure of Arabidopsis ARID5 ARID-PHD cassette in complex with H3K4me3 peptide and DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 

wwPDB Validation 3D Report Full Report



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 

  • DOI: 10.1105/tpc.19.00944
  • Structures With Same Primary Citation

  • 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. Her ...

    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 ISWI chromatin remodeling complexes in Arabidopsis thaliana. We found that 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 CITY: Beijing POSTAL_CODE: 102206 China [CN] hexinjian@nibs.ac.cn.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AT-rich interactive domain-containing protein 4
A
204Arabidopsis thalianaMutation(s): 0 
Gene Names: ARID4At3g43240F7K15.90
Find proteins for Q6NQ79 (Arabidopsis thaliana)
Go to UniProtKB:  Q6NQ79
Protein Feature View
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
15-mer peptide from Histone H3.2
P
15Arabidopsis thalianaMutation(s): 0 
Gene Names: 
Find proteins for P59226 (Arabidopsis thaliana)
Go to UniProtKB:  P59226
Protein Feature View
  • Reference Sequence
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*TP*TP*AP*GP*AP*TP*CP*TP*AP*AP*A)-3')B, C12synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
PL-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.173α = 90
b = 59.428β = 90
c = 92.958γ = 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

  • Deposited Date: 2020-01-13 
  • Released Date: 2020-06-03 
  • Deposition Author(s): Liu, R., Du, J.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31622032

Revision History 

  • Version 1.0: 2020-06-03
    Type: Initial release