Crystal structure of SUVH9

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report

This is version 1.1 of the entry. See complete history


SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation.

Johnson, L.M.Du, J.Hale, C.J.Bischof, S.Feng, S.Chodavarapu, R.K.Zhong, X.Marson, G.Pellegrini, M.Segal, D.J.Patel, D.J.Jacobsen, S.E.

(2014) Nature 507: 124-128

  • DOI: https://doi.org/10.1038/nature12931
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    RNA-directed DNA methylation in Arabidopsis thaliana depends on the upstream synthesis of 24-nucleotide small interfering RNAs (siRNAs) by RNA POLYMERASE IV (Pol IV) and downstream synthesis of non-coding transcripts by Pol V. Pol V transcripts are thought to interact with siRNAs which then recruit DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2) to methylate DNA. The SU(VAR)3-9 homologues SUVH2 and SUVH9 act in this downstream step but the mechanism of their action is unknown. Here we show that genome-wide Pol V association with chromatin redundantly requires SUVH2 and SUVH9. Although SUVH2 and SUVH9 resemble histone methyltransferases, a crystal structure reveals that SUVH9 lacks a peptide-substrate binding cleft and lacks a properly formed S-adenosyl methionine (SAM)-binding pocket necessary for normal catalysis, consistent with a lack of methyltransferase activity for these proteins. SUVH2 and SUVH9 both contain SRA (SET- and RING-ASSOCIATED) domains capable of binding methylated DNA, suggesting that they function to recruit Pol V through DNA methylation. Consistent with this model, mutation of DNA METHYLTRANSFERASE 1 (MET1) causes loss of DNA methylation, a nearly complete loss of Pol V at its normal locations, and redistribution of Pol V to sites that become hypermethylated. Furthermore, tethering SUVH9 [corrected] with a zinc finger to an unmethylated site is sufficient to recruit Pol V and establish DNA methylation and gene silencing. These results indicate that Pol V is recruited to DNA methylation through the methyl-DNA binding SUVH2 and SUVH9 proteins, and our mechanistic findings suggest a means for selectively targeting regions of plant genomes for epigenetic silencing.

  • Organizational Affiliation

    Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH9518Arabidopsis thalianaMutation(s): 0 
Gene Names: At4g13460SDG22SET22SUVH9T6G15.10
Find proteins for Q9T0G7 (Arabidopsis thaliana)
Explore Q9T0G7 
Go to UniProtKB:  Q9T0G7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9T0G7
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.679α = 90
b = 84.197β = 90
c = 99.359γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHENIXmodel building
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-22
    Type: Initial release
  • Version 1.1: 2014-03-12
    Changes: Database references