Chromo Domain of Human Histone-Lysine N-Methyltransferase SUV39H1

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report

This is version 1.6 of the entry. See complete history


Crystal Structure of the Human SUV39H1 Chromodomain and Its Recognition of Histone H3K9me2/3.

Wang, T.Xu, C.Liu, Y.Fan, K.Li, Z.Sun, X.Ouyang, H.Zhang, X.Zhang, J.Li, Y.Mackenzie, F.Min, J.Tu, X.

(2012) PLoS One 7: e52977-e52977

  • DOI: https://doi.org/10.1371/journal.pone.0052977
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    SUV39H1, the first identified histone lysine methyltransferase in human, is involved in chromatin modification and gene regulation. SUV39H1 contains a chromodomain in its N-terminus, which potentially plays a role in methyl-lysine recognition and SUV39H1 targeting. In this study, the structure of the chromodomain of human SUV39H1 was determined by X-ray crystallography. The SUV39H1 chromodomain displays a generally conserved structure fold compared with other solved chromodomains. However, different from other chromodomains, the SUV39H1 chromodomain possesses a much longer helix at its C-terminus. Furthermore, the SUV39H1 chromodomain was shown to recognize histone H3K9me2/3 specifically.

  • Organizational Affiliation

    Hefei National Laboratory for Physical Sciences at Microscale, School of Life Science, University of Science and Technology of China, Hefei, Anhui, People's Republic of China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase SUV39H1
A, B, C
64Homo sapiensMutation(s): 0 
Gene Names: KMT1ASUV39HSUV39H1
EC: (PDB Primary Data), (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O43463 (Homo sapiens)
Explore O43463 
Go to UniProtKB:  O43463
PHAROS:  O43463
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43463
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.528α = 90
b = 99.528β = 90
c = 118.321γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
Locallydata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2010-06-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-01-23
    Changes: Database references
  • Version 1.3: 2013-01-30
    Changes: Database references
  • Version 1.4: 2015-01-28
    Changes: Other
  • Version 1.5: 2017-11-08
    Changes: Refinement description
  • Version 1.6: 2023-09-06
    Changes: Data collection, Database references, Refinement description