4JCJ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.254 

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

  • 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-termin ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Insulin gene enhancer protein ISL-1,LIM domain-binding protein 1
A, B, C
173Mus musculusMutation(s): 0 
Gene Names: Isl1, Ldb1 (Nli)
Find proteins for P61372 (Mus musculus)
Go to UniProtKB:  P61372
Find proteins for P70662 (Mus musculus)
Go to UniProtKB:  P70662
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.254 
  • Space Group: P 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 57.310α = 90.00
b = 56.639β = 90.00
c = 179.342γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
ADSCdata collection
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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