4AYA

Crystal structure of ID2 HLH homodimer at 2.1A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

A Divalent Ion is Crucial in the Structure and Dominant-Negative Function of Id Proteins, a Class of Helix-Loop-Helix Transcription Regulators.

Wong, M.V.Jiang, S.Palasingam, P.Kolatkar, P.R.

(2012) PLoS One 7: 48591

  • DOI: https://doi.org/10.1371/journal.pone.0048591
  • Primary Citation of Related Structures:  
    4AYA

  • PubMed Abstract: 

    Inhibitors of DNA binding and differentiation (ID) proteins, a dominant-negative group of helix-loop-helix (HLH) transcription regulators, are well-characterized key players in cellular fate determination during development in mammals as well as Drosophila. Although not oncogenes themselves, their upregulation by various oncogenic proteins (such as Ras, Myc) and their inhibitory effects on cell cycle proteins (such as pRb) hint at their possible roles in tumorigenesis. Furthermore, their potency as inhibitors of cellular differentiation, through their heterodimerization with subsequent inactivation of the ubiquitous E proteins, suggest possible novel roles in engineering induced pluripotent stem cells (iPSCs). We present the high-resolution 2.1Å crystal structure of ID2 (HLH domain), coupled with novel biochemical insights in the presence of a divalent ion, possibly calcium (Ca2+), in the loop of ID proteins, which appear to be crucial for the structure and activity of ID proteins. These new insights will pave the way for new rational drug designs, in addition to current synthetic peptide options, against this potent player in tumorigenesis as well as more efficient ways for stem cells reprogramming.


  • Organizational Affiliation

    Laboratory for Structural Biochemistry, Genome Institute of Singapore, Singapore, Singapore.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-BINDING PROTEIN INHIBITOR ID-2
A, B
97Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q02363 (Homo sapiens)
Explore Q02363 
Go to UniProtKB:  Q02363
GTEx:  ENSG00000115738 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02363
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.622α = 90
b = 51.622β = 90
c = 111.474γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-14
    Type: Initial release