Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 21.83 kDa 
• Atom Count: 900 
• Residue Count: 107 
• Unique protein chains: 1

4AYA

Crystal structure of ID2 HLH homodimer at 2.1A resolution

• DOI: 10.2210/pdb4AYA/pdb

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-06-19 Released: 2012-11-14 
• Deposition Author(s): Wong, M.V., Jiang, S., Palasingam, P., Kolatkar, P.R.

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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 

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

• PubMed: 23119064 
• DOI: 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-BINDING PROTEIN INHIBITOR ID-2	A, B	97	Homo sapiens	Mutation(s): 0  Gene Names: ID2, BHLHB26
Find proteins for Q02363 (Homo sapiens) Explore Q02363  Go to UniProtKB:  Q02363
NIH Common Fund Data Resources
PHAROS:  Q02363 GTEx:  ENSG00000115738

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	A	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
K	A, B	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

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 = 51.622	α = 90
b = 51.622	β = 90
c = 111.474	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-06-19 
• Released Date: 2012-11-14 
Deposition Author(s): Wong, M.V., Jiang, S., Palasingam, P., Kolatkar, P.R.

Revision History 

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