3DM1

Crystal structure of the complex of human chromobox homolog 3 (CBX3) with peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis of the chromodomain of Cbx3 bound to methylated peptides from histone h1 and G9a.

Ruan, J.Ouyang, H.Amaya, M.F.Ravichandran, M.Loppnau, P.Min, J.Zang, J.

(2012) PLoS One 7: e35376-e35376

  • DOI: 10.1371/journal.pone.0035376
  • Primary Citation of Related Structures:  
    3TZD, 3DM1

  • PubMed Abstract: 
  • HP1 proteins are highly conserved heterochromatin proteins, which have been identified to be structural adapters assembling a variety of macromolecular complexes involved in regulation of gene expression, chromatin remodeling and heterochromatin form ...

    HP1 proteins are highly conserved heterochromatin proteins, which have been identified to be structural adapters assembling a variety of macromolecular complexes involved in regulation of gene expression, chromatin remodeling and heterochromatin formation. Much evidence shows that HP1 proteins interact with numerous proteins including methylated histones, histone methyltransferases and so on. Cbx3 is one of the paralogues of HP1 proteins, which has been reported to specifically recognize trimethylated histone H3K9 mark, and a consensus binding motif has been defined for the Cbx3 chromodomain.


    Organizational Affiliation

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



Macromolecules
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase, H3 lysine-9 specific 3BDFH12N/AMutation(s): 0 
Find proteins for Q96KQ7 (Homo sapiens)
Explore Q96KQ7 
Go to UniProtKB:  Q96KQ7
NIH Common Fund Data Resources
PHAROS  Q96KQ7
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Chromobox protein homolog 3ACEG58Homo sapiensMutation(s): 0 
Gene Names: CBX3
Find proteins for Q13185 (Homo sapiens)
Explore Q13185 
Go to UniProtKB:  Q13185
NIH Common Fund Data Resources
PHAROS  Q13185
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
B,D,F,HL-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.671α = 90
b = 83.671β = 90
c = 110.288γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-08-19
    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: 2017-10-25
    Changes: Refinement description