crystal structure of AGD1-4 of Arabidopsis AGDP3

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.246 

wwPDB Validation   3D Report Full Report

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The H3K9me2-binding protein AGDP3 limits DNA methylation and transcriptional gene silencing in Arabidopsis.

Zhou, X.Wei, M.Nie, W.Xi, Y.Peng, L.Zheng, Q.Tang, K.Satheesh, V.Wang, Y.Luo, J.Du, X.Liu, R.Yang, Z.La, H.Zhong, Y.Yang, Y.Zhu, J.K.Du, J.Lei, M.

(2022) J Integr Plant Biol 64: 2385-2395

  • DOI: https://doi.org/10.1111/jipb.13369
  • Primary Citation of Related Structures:  
    7YT9, 7YTA

  • PubMed Abstract: 

    DNA methylation, a conserved epigenetic mark, is critical for tuning temporal and spatial gene expression. The Arabidopsis thaliana DNA glycosylase/lyase REPRESSOR OF SILENCING 1 (ROS1) initiates active DNA demethylation and is required to prevent DNA hypermethylation at thousands of genomic loci. However, how ROS1 is recruited to specific loci is not well understood. Here, we report the discovery of Arabidopsis AGENET Domain Containing Protein 3 (AGDP3) as a cellular factor that is required to prevent gene silencing and DNA hypermethylation. AGDP3 binds to H3K9me2 marks in its target DNA via its AGD12 cassette. Analysis of the crystal structure of the AGD12 cassette of AGDP3 in complex with an H3K9me2 peptide revealed that dimethylated H3K9 and unmodified H3K4 are specifically anchored into two different surface pockets. A histidine residue located in the methyllysine binding aromatic cage provides AGDP3 with pH-dependent H3K9me2 binding capacity. Our results uncover a molecular mechanism for the regulation of DNA demethylation by the gene silencing mark H3K9me2.

  • Organizational Affiliation

    Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AGD1-4 of Arabidopsis AGDP3
A, B
291Arabidopsis thalianaMutation(s): 3 
Gene Names: DUF6ATDUF6At2g47230T8I13.7
Find proteins for F4IL23 (Arabidopsis thaliana)
Explore F4IL23 
Go to UniProtKB:  F4IL23
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF4IL23
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.246 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.538α = 90
b = 129.205β = 90
c = 167.049γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Other governmentChinaJCYJ20200109110403829

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-12
    Type: Initial release
  • Version 1.1: 2023-01-11
    Changes: Database references
  • Version 1.2: 2024-05-29
    Changes: Data collection