1RUT

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 

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
  • Primary Citation of Related Structures:  
    1RUT

  • 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 nuclear adaptor protein LIM domain-binding protein-1 (Ldb1) ...

    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 D Biol Crystallogr 59: 1484
    Organizational Affiliation: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fusion protein of Lmo4 protein and LIM domain-binding protein 1 X188Mus musculusMutation(s): 2 
Gene Names: lmo4, Ldb1
Find proteins for P70662 (Mus musculus)
Explore P70662 
Go to UniProtKB:  P70662
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 
  • Space Group: P 3 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.344α = 90
b = 61.344β = 90
c = 93.159γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

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