6A5N

Crystal structure of Arabidopsis thaliana SUVH6 in complex with methylated DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Mechanistic insights into plant SUVH family H3K9 methyltransferases and their binding to context-biased non-CG DNA methylation.

Li, X.Harris, C.J.Zhong, Z.Chen, W.Liu, R.Jia, B.Wang, Z.Li, S.Jacobsen, S.E.Du, J.

(2018) Proc. Natl. Acad. Sci. U.S.A. --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH6
A
527Arabidopsis thalianaMutation(s): 1 
Gene Names: SUVH6 (SDG23, SET23)
EC: 2.1.1.43
Find proteins for Q8VZ17 (Arabidopsis thaliana)
Go to UniProtKB:  Q8VZ17
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*AP*GP*TP*AP*CP*TP*(5CM)P*AP*GP*CP*AP*GP*T)-3')C14synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*AP*CP*TP*GP*CP*TP*GP*AP*GP*TP*AP*CP*T)-3')D14synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5CM
Query on 5CM
C
DNA LINKINGC10 H16 N3 O7 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.230 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 74.137α = 90.00
b = 79.443β = 90.00
c = 107.845γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data reduction
PHENIXphasing
HKL-3000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-06-24 
  • Released Date: 2018-08-29 
  • Deposition Author(s): Li, X., Du, J.

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

Revision History 

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 1.1: 2018-09-19
    Type: Data collection, Database references