3N9N

ceKDM7A from C.elegans, complex with H3K4me3K9me2 peptide and NOG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into a dual-specificity histone demethylase ceKDM7A from Caenorhabditis elegans

Yang, Y.Hu, L.Wang, P.Hou, H.Lin, Y.Liu, Y.Li, Z.Gong, R.Feng, X.Zhou, L.Zhang, W.Dong, Y.Yang, H.Lin, H.Wang, Y.Chen, C.D.Xu, Y.

(2010) Cell Res 20: 886-898

  • DOI: https://doi.org/10.1038/cr.2010.86
  • Primary Citation of Related Structures:  
    3N9L, 3N9M, 3N9N, 3N9O, 3N9P, 3N9Q

  • PubMed Abstract: 

    Histone lysine methylation can be removed by JmjC domain-containing proteins in a sequence- and methylation-state-specific manner. However, how substrate specificity is determined and how the enzymes are regulated were largely unknown. We recently found that ceKDM7A, a PHD- and JmjC domain-containing protein, is a histone demethylase specific for H3K9me2 and H3K27me2, and the PHD finger binding to H3K4me3 guides the demethylation activity in vivo. To provide structural insight into the molecular mechanisms for the enzymatic activity and the function of the PHD finger, we solved six crystal structures of the enzyme in apo form and in complex with single or two peptides containing various combinations of H3K4me3, H3K9me2, and H3K27me2 modifications. The structures indicate that H3K9me2 and H3K27me2 interact with ceKDM7A in a similar fashion, and that the peptide-binding specificity is determined by a network of specific interactions. The geometrical measurement of the structures also revealed that H3K4me3 associated with the PHD finger and H3K9me2 bound to the JmjC domain are from two separate molecules, suggesting a trans-histone peptide-binding mechanism. Thus, our systemic structural studies reveal not only the substrate recognition by the catalytic domain but also more importantly, the molecular mechanism of dual specificity of ceDKM7A for both H3K9me2 and H3K27me2.


  • Organizational Affiliation

    Cancer Institute, Shanghai Cancer Center, Fudan University, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative uncharacterized protein528Caenorhabditis elegansMutation(s): 0 
Gene Names: F29B9.2
EC: 1.14.11.27 (PDB Primary Data), 1.14.11 (UniProt)
UniProt
Find proteins for Q9GYI0 (Caenorhabditis elegans)
Explore Q9GYI0 
Go to UniProtKB:  Q9GYI0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9GYI0
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3 peptide
B, C
32Caenorhabditis elegansMutation(s): 0 
UniProt
Find proteins for P08898 (Caenorhabditis elegans)
Explore P08898 
Go to UniProtKB:  P08898
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08898
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.4α = 90
b = 85.543β = 90
c = 102.55γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
PHENIXrefinement
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: 2010-06-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description