1RUT

Complex of LMO4 LIM domains 1 and 2 with the ldb1 LID domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Tandem LIM domains provide synergistic binding in the LMO4:Ldb1 complex

Deane, J.E.Ryan, D.P.Sunde, M.Maher, M.J.Guss, J.M.Visvader, J.E.Matthews, J.M.

(2004) Embo J. 23: 3589-3598

  • DOI: 10.1038/sj.emboj.7600376

  • PubMed Abstract: 
  • Nuclear LIM-only (LMO) and LIM-homeodomain (LIM-HD) proteins have important roles in cell fate determination, organ development and oncogenesis. These proteins contain tandemly arrayed LIM domains that bind the LIM interaction domain (LID) of the nuc ...

    Nuclear LIM-only (LMO) and LIM-homeodomain (LIM-HD) proteins have important roles in cell fate determination, organ development and oncogenesis. These proteins contain tandemly arrayed LIM domains that bind the LIM interaction domain (LID) of the nuclear adaptor protein LIM domain-binding protein-1 (Ldb1). We have determined a high-resolution X-ray crystal structure of LMO4, a putative breast oncoprotein, in complex with Ldb1-LID, providing the first example of a tandem LIM:Ldb1-LID complex and the first structure of a type-B LIM domain. The complex possesses a highly modular structure with Ldb1-LID binding in an extended manner across both LIM domains of LMO4. The interface contains extensive hydrophobic and electrostatic interactions and multiple backbone-backbone hydrogen bonds. A mutagenic screen of Ldb1-LID, assessed by yeast two-hybrid and competition ELISA analysis, identified key features at the interface and revealed that the interaction is tolerant to mutation. These combined properties provide a mechanism for the binding of Ldb1 to numerous LMO and LIM-HD proteins. Furthermore, the modular extended interface may form a general mode of binding to tandem LIM domains.


    Related Citations: 
    • Crystallization of FLINC4, an intramolecular LMO4-ldb1 complex
      Deane, J.E.,Maher, M.J.,Langley, D.B.,Graham, S.C.,Visvader, J.E.,Guss, J.M.,Matthews, J.M.
      (2003) Acta Crystallogr.,Sect.D 59: 1484


    Organizational Affiliation

    School of Molecular and Microbial Biosciences, University of Sydney, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fusion protein of Lmo4 protein and LIM domain-binding protein 1
X
188Mus musculusMutations: C37S, C49S
Gene Names: Ldb1 (Nli)
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 
X
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.155 
  • Space Group: P 3 1 2
Unit Cell:
Length (Å)Angle (°)
a = 61.344α = 90.00
b = 61.344β = 90.00
c = 93.159γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
REFMACrefinement
SOLVEphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-10-12
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-08-23
    Type: Source and taxonomy