5ZWX

Crystal structure of Raphanus sativus AGDP1 AGD12 in complex with an H3K9me2 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Arabidopsis AGDP1 links H3K9me2 to DNA methylation in heterochromatin

Zhang, C.Du, X.Tang, K.Yang, Z.Pan, L.Zhu, P.Luo, J.Jiang, Y.Zhang, H.Wan, H.Wang, X.Wu, F.Tao, W.A.He, X.J.Zhang, H.Bressan, R.A.Du, J.Zhu, J.K.

(2018) Nat Commun 9: 4547-4547

  • DOI: https://doi.org/10.1038/s41467-018-06965-w
  • Primary Citation of Related Structures:  
    5ZWX, 5ZWZ

  • PubMed Abstract: 

    Heterochromatin is a tightly packed form of chromatin that is associated with DNA methylation and histone 3 lysine 9 methylation (H3K9me). Here, we identify an H3K9me2-binding protein, Agenet domain (AGD)-containing p1 (AGDP1), in Arabidopsis thaliana. Here we find that AGDP1 can specifically recognize the H3K9me2 mark by its three pairs of tandem AGDs. We determine the crystal structure of the Agenet domain 1 and 2 cassette (AGD12) of Raphanus sativus AGDP1 in complex with an H3K9me2 peptide. In the complex, the histone peptide adopts a unique helical conformation. AGD12 specifically recognizes the H3K4me0 and H3K9me2 marks by hydrogen bonding and hydrophobic interactions. In addition, we find that AGDP1 is required for transcriptional silencing, non-CG DNA methylation, and H3K9 dimethylation at some loci. ChIP-seq data show that AGDP1 preferentially occupies long transposons and is associated with heterochromatin marks. Our findings suggest that, as a heterochromatin-binding protein, AGDP1 links H3K9me2 to DNA methylation in heterochromatin regions.


  • Organizational Affiliation

    National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 201602, Shanghai, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DUF724 domain-containing protein 6-likeA,
C [auth B]
161Raphanus sativusMutation(s): 0 
UniProt
Find proteins for A0A493R6M0 (Raphanus sativus)
Explore A0A493R6M0 
Go to UniProtKB:  A0A493R6M0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A493R6M0
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
H3(1-15)K9me2 peptideB [auth P],
D [auth Q]
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  2 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A,
C [auth B]
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
MLY
Query on MLY
B [auth P],
D [auth Q]
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.653α = 90
b = 54.981β = 99.72
c = 83.576γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2018-11-14 
  • Deposition Author(s): Du, X., Du, J.

Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China2016YFA0503200

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-14
    Type: Initial release