4JCJ

Crystal structure of Isl1 LIM domains with Ldb1 LIM-interaction domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.256 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

A structural basis for the regulation of the LIM-homeodomain protein islet 1 (Isl1) by intra- and intermolecular interactions.

Gadd, M.S.Jacques, D.A.Nisevic, I.Craig, V.J.Kwan, A.H.Guss, J.M.Matthews, J.M.

(2013) J Biol Chem 288: 21924-21935

  • DOI: 10.1074/jbc.M113.478586
  • Primary Citation of Related Structures:  
    4JCJ

  • PubMed Abstract: 
  • Islet 1 (Isl1) is a transcription factor of the LIM-homeodomain (LIM-HD) protein family and is essential for many developmental processes. LIM-HD proteins all contain two protein-interacting LIM domains, a DNA-binding homeodomain (HD), and a C-terminal region ...

    Islet 1 (Isl1) is a transcription factor of the LIM-homeodomain (LIM-HD) protein family and is essential for many developmental processes. LIM-HD proteins all contain two protein-interacting LIM domains, a DNA-binding homeodomain (HD), and a C-terminal region. In Isl1, the C-terminal region also contains the LIM homeobox 3 (Lhx3)-binding domain (LBD), which interacts with the LIM domains of Lhx3. The LIM domains of Isl1 have been implicated in inhibition of DNA binding potentially through an intramolecular interaction with or close to the HD. Here we investigate the LBD as a candidate intramolecular interaction domain. Competitive yeast-two hybrid experiments indicate that the LIM domains and LBD from Isl1 can interact with apparently low affinity, consistent with no detection of an intermolecular interaction in the same system. Nuclear magnetic resonance studies show that the interaction is specific, whereas substitution of the LBD with peptides of the same amino acid composition but different sequence is not specific. We solved the crystal structure of a similar but higher affinity complex between the LIM domains of Isl1 and the LIM interaction domain from the LIM-HD cofactor protein LIM domain-binding protein 1 (Ldb1) and used these coordinates to generate a homology model of the intramolecular interaction that indicates poorer complementarity for the weak intramolecular interaction. The intramolecular interaction in Isl1 may provide protection against aggregation, minimize unproductive DNA binding, and facilitate cofactor exchange within the cell.


    Organizational Affiliation

    School of Molecular Bioscience, Building G08, University of Sydney, New South Wales 2006, Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Insulin gene enhancer protein ISL-1,LIM domain-binding protein 1A, B, C173Mus musculusMutation(s): 0 
Gene Names: Isl1Ldb1Nli
UniProt
Find proteins for P61372 (Mus musculus)
Explore P61372 
Go to UniProtKB:  P61372
Find proteins for P70662 (Mus musculus)
Explore P70662 
Go to UniProtKB:  P70662
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.256 
  • Space Group: P 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.31α = 90
b = 56.639β = 90
c = 179.342γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-19
    Type: Initial release
  • Version 1.1: 2013-10-09
    Changes: Database references
  • Version 1.2: 2017-05-31
    Changes: Structure summary
  • Version 1.3: 2017-06-21
    Changes: Database references
  • Version 1.4: 2017-11-15
    Changes: Refinement description