PDBsum entry 1m3v

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protein metals links
Metal binding protein PDB id
Jmol PyMol
Protein chain
122 a.a. *
_ZN ×2
* Residue conservation analysis
PDB id:
Name: Metal binding protein
Title: Flin4: fusion of the lim binding domain of ldb1 and the n- terminal lim domain of lmo4
Structure: Fusion of the lim interacting domain of ldb1 and the n-terminal lim domain of lmo4. Chain: a. Synonym: flin4. Engineered: yes. Mutation: yes. Other_details: fusion protein comprises lim domain transcription factor lmo4 (residues 16-86) via glycine- rich linker (ggsgghmgsgg), lim domain-binding protein 1
Source: Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
NMR struc: 20 models
Authors: J.E.Deane,J.P.Mackay,A.H.Y.Kwan,E.Y.Sum,J.E.Visvader, J.M.Matthews
Key ref: J.E.Deane et al. (2003). Structural basis for the recognition of ldb1 by the N-terminal LIM domains of LMO2 and LMO4. EMBO J, 22, 2224-2233. PubMed id: 12727888
30-Jun-02     Release date:   13-May-03    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P70662  (LDB1_MOUSE) -  LIM domain-binding protein 1
411 a.a.
122 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 77 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     zinc ion binding     1 term  


EMBO J 22:2224-2233 (2003)
PubMed id: 12727888  
Structural basis for the recognition of ldb1 by the N-terminal LIM domains of LMO2 and LMO4.
J.E.Deane, J.P.Mackay, A.H.Kwan, E.Y.Sum, J.E.Visvader, J.M.Matthews.
LMO2 and LMO4 are members of a small family of nuclear transcriptional regulators that are important for both normal development and disease processes. LMO2 is essential for hemopoiesis and angiogenesis, and inappropriate overexpression of this protein leads to T-cell leukemias. LMO4 is developmentally regulated in the mammary gland and has been implicated in breast oncogenesis. Both proteins comprise two tandemly repeated LIM domains. LMO2 and LMO4 interact with the ubiquitous nuclear adaptor protein ldb1/NLI/CLIM2, which associates with the LIM domains of LMO and LIM homeodomain proteins via its LIM interaction domain (ldb1-LID). We report the solution structures of two LMO:ldb1 complexes (PDB: 1M3V and 1J2O) and show that ldb1-LID binds to the N-terminal LIM domain (LIM1) of LMO2 and LMO4 in an extended conformation, contributing a third strand to a beta-hairpin in LIM1 domains. These findings constitute the first molecular definition of LIM-mediated protein-protein interactions and suggest a mechanism by which ldb1 can bind a variety of LIM domains that share low sequence homology.

Literature references that cite this PDB file's key reference

  PubMed id Reference
23303138 J.M.Matthews, K.Lester, S.Joseph, and D.J.Curtis (2012).
LIM-domain-only proteins in cancer.
  Nat Rev Cancer, 13, 111-122.  
21076045 K.El Omari, S.J.Hoosdally, K.Tuladhar, D.Karia, P.Vyas, R.Patient, C.Porcher, and E.J.Mancini (2011).
Structure of the leukemia oncogene LMO2: implications for the assembly of a hematopoietic transcription factor complex.
  Blood, 117, 2146-2156.
PDB codes: 2xjy 2xjz
20563763 L.E.Wilkinson-White, S.Dastmalchi, A.H.Kwan, D.P.Ryan, J.P.Mackay, and J.M.Matthews (2010).
1H, 15N and 13C assignments of an intramolecular Lmo2-LIM2/Ldb1-LID complex.
  Biomol NMR Assign, 4, 203-206.
PDB code: 2l3k
19228115 T.Susa, A.Ishikawa, L.Y.Cai, T.Kato, K.Matsumoto, K.Kitahara, R.Kurokawa, T.Ono, and Y.Kato (2010).
The highly related LIM factors, LMO1, LMO3 and LMO4, play different roles in the regulation of the pituitary glycoprotein hormone alpha-subunit (alpha GSU) gene.
  Biosci Rep, 30, 51-58.  
19095651 J.A.Lowry, R.Gamsjaeger, S.Y.Thong, W.Hung, A.H.Kwan, G.Broitman-Maduro, J.M.Matthews, M.Maduro, and J.P.Mackay (2009).
Structural Analysis of MED-1 Reveals Unexpected Diversity in the Mechanism of DNA Recognition by GATA-type Zinc Finger Domains.
  J Biol Chem, 284, 5827-5835.
PDB code: 2kae
19666821 M.R.Song, Y.Sun, A.Bryson, G.N.Gill, S.M.Evans, and S.L.Pfaff (2009).
Islet-to-LMO stoichiometries control the function of transcription complexes that specify motor neuron and V2a interneuron identity.
  Development, 136, 2923-2932.  
18694769 U.Heberlein, L.T.Tsai, D.Kapfhamer, and A.W.Lasek (2009).
Drosophila, a genetic model system to study cocaine-related behaviors: a review with focus on LIM-only proteins.
  Neuropharmacology, 56, 97.  
19199338 Y.Kato, T.Kato, T.Ono, T.Susa, K.Kitahara, and K.Matsumoto (2009).
Intracellular localization of porcine single-strand binding protein 2.
  J Cell Biochem, 106, 912-919.  
19117955 Y.Yang, X.Wang, C.A.Hawkins, K.Chen, J.Vaynberg, X.Mao, Y.Tu, X.Zuo, J.Wang, Y.X.Wang, C.Wu, N.Tjandra, and J.Qin (2009).
Structural Basis of Focal Adhesion Localization of LIM-only Adaptor PINCH by Integrin-linked Kinase.
  J Biol Chem, 284, 5836-5844.  
19074270 B.P.Chiswell, R.Zhang, J.W.Murphy, T.J.Boggon, and D.A.Calderwood (2008).
The structural basis of integrin-linked kinase-PINCH interactions.
  Proc Natl Acad Sci U S A, 105, 20677-20682.
PDB code: 3f6q
18583962 M.Bhati, C.Lee, A.L.Nancarrow, M.Lee, V.J.Craig, I.Bach, J.M.Guss, J.P.Mackay, and J.M.Matthews (2008).
Implementing the LIM code: the structural basis for cell type-specific assembly of LIM-homeodomain complexes.
  EMBO J, 27, 2018-2029.
PDB codes: 2jtn 2rgt
18689881 S.Zenvirt, Y.Nevo-Caspi, S.Rencus-Lazar, and D.Segal (2008).
Drosophila LIM-only is a positive regulator of transcription during thoracic bristle development.
  Genetics, 179, 1989-1999.  
17878155 E.Lécuyer, S.Larivière, M.C.Sincennes, A.Haman, R.Lahlil, M.Todorova, M.Tremblay, B.C.Wilkes, and T.Hoang (2007).
Protein stability and transcription factor complex assembly determined by the SCL-LMO2 interaction.
  J Biol Chem, 282, 33649-33658.  
17001033 C.M.Jeffries, S.C.Graham, P.H.Stokes, C.A.Collyer, J.M.Guss, and J.M.Matthews (2006).
Stabilization of a binary protein complex by intein-mediated cyclization.
  Protein Sci, 15, 2612-2618.
PDB code: 2dfy
15343268 J.E.Deane, D.P.Ryan, M.Sunde, M.J.Maher, J.M.Guss, J.E.Visvader, and J.M.Matthews (2004).
Tandem LIM domains provide synergistic binding in the LMO4:Ldb1 complex.
  EMBO J, 23, 3589-3598.
PDB code: 1rut
15520811 J.L.Kadrmas, and M.C.Beckerle (2004).
The LIM domain: from the cytoskeleton to the nucleus.
  Nat Rev Mol Cell Biol, 5, 920-931.  
12876360 J.E.Deane, M.J.Maher, D.B.Langley, S.C.Graham, J.E.Visvader, J.M.Guss, and J.M.Matthews (2003).
Crystallization of FLINC4, an intramolecular LMO4-ldb1 complex.
  Acta Crystallogr D Biol Crystallogr, 59, 1484-1486.  
14647207 J.M.Matthews, and J.E.Visvader (2003).
LIM-domain-binding protein 1: a multifunctional cofactor that interacts with diverse proteins.
  EMBO Rep, 4, 1132-1137.  
12925972 K.D.Sutherland, J.E.Visvader, D.Y.Choong, E.Y.Sum, G.J.Lindeman, and I.G.Campbell (2003).
Mutational analysis of the LMO4 gene, encoding a BRCA1-interacting protein, in breast carcinomas.
  Int J Cancer, 107, 155-158.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.