2LXD

Backbone 1H, 13C, and 15N Chemical Shift Assignments for LMO2(LIM2)-Ldb1(LID)

• PDB DOI: https://doi.org/10.2210/pdb2LXD/pdb
• Entry: 2LXD supersedes: 2L3K
• BMRB: 16779

• Classification: TRANSCRIPTION
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-08-20 Released: 2012-09-12 
• Deposition Author(s): Dastmalchi, S., Wilkinson-White, L., Kwan, A.H., Gamsjaeger, R., Mackay, J.P., Matthews, J.M.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Solution structure of a tethered Lmo2(LIM2) /Ldb1(LID) complex.

Dastmalchi, S., Wilkinson-White, L., Kwan, A.H., Gamsjaeger, R., Mackay, J.P., Matthews, J.M.

(2012) Protein Sci 21: 1768-1774

• PubMed: 22936624 
• DOI: https://doi.org/10.1002/pro.2153
• Primary Citation of Related Structures:  
  2LXD


• PubMed Abstract: 
  

  LIM-only protein 2, Lmo2, is a regulatory protein that is essential for hematopoietic development and inappropriate overexpression of Lmo2 in T-cells contributes to T-cell leukemia. It exerts its functions by mediating protein-protein interactions and nucleating multicomponent transcriptional complexes. Lmo2 interacts with LIM domain binding protein 1 (Ldb1) through the tandem LIM domains of Lmo2 and the LIM interaction domain (LID) of Ldb1. Here, we present the solution structure of the LIM2 domain of Lmo2 bound to Ldb1(LID) . The ordered regions of Ldb1 in this complex correspond well with binding hotspots previously defined by mutagenic studies. Comparisons of this Lmo2(LIM2) -Ldb1(LID) structure with previously determined structures of the Lmo2/Ldb1(LID) complexes lead to the conclusion that modular binding of tandem LIM domains in Lmo2 to tandem linear motifs in Ldb1 is accompanied by several disorder-to-order transitions and/or conformational changes in both proteins.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 13.94 kDa 
• Atom Count: 954 
• Modelled Residue Count: 123 
• Deposited Residue Count: 125 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rhombotin-2,LIM domain-binding protein 1	A	125	Mus musculus	Mutation(s): 1  Gene Names: Lmo2, Rbtn-2, Rbtn2, Rhom-2, Ldb1, Nli
UniProt
Find proteins for P70662 (Mus musculus) Explore P70662  Go to UniProtKB:  P70662
Find proteins for P25801 (Mus musculus) Explore P25801  Go to UniProtKB:  P25801
UniProt Groups	P70662P25801

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-12 
Deposition Author(s): Dastmalchi, S., Wilkinson-White, L., Kwan, A.H., Gamsjaeger, R., Mackay, J.P., Matthews, J.M.
• This entry supersedes: 2L3K

Revision History  

• Version 1.0: 2012-09-12
  Type: Initial release
  
• Version 1.1: 2020-01-15
  Changes: Data collection, Database references, Source and taxonomy, Structure summary
• Version 1.2: 2022-08-24
  Changes: Database references, Derived calculations
• Version 1.3: 2023-06-14
  Changes: Other