2XJY

Crystal structure of the LMO2:LDB1-LID complex, P21 crystal form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the Leukemia Oncogene Lmo2: Implications for the Assembly of a Hematopoietic Transcription Factor Complex.

El Omari, K.Hoosdally, S.J.Tuladhar, K.Karia, D.Vyas, P.Patient, R.Porcher, C.Mancini, E.J.

(2011) Blood 117: 2146

  • DOI: 10.1182/blood-2010-07-293357
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The LIM only protein 2 (LMO2) is a key regulator of hematopoietic stem cell development whose ectopic expression in T cells leads to the onset of acute lymphoblastic leukemia. Through its LIM domains, LMO2 is thought to function as the scaffold for a ...

    The LIM only protein 2 (LMO2) is a key regulator of hematopoietic stem cell development whose ectopic expression in T cells leads to the onset of acute lymphoblastic leukemia. Through its LIM domains, LMO2 is thought to function as the scaffold for a DNA-binding transcription regulator complex, including the basic helix-loop-helix proteins SCL/TAL1 and E47, the zinc finger protein GATA-1, and LIM-domain interacting protein LDB1. To understand the role of LMO2 in the formation of this complex and ultimately to dissect its function in normal and aberrant hematopoiesis, we solved the crystal structure of LMO2 in complex with the LID domain of LDB1 at 2.4 Å resolution. We observe a largely unstructured LMO2 kept in register by the LID binding both LIM domains. Comparison of independently determined crystal structures of LMO2 reveals large movements around a conserved hinge between the LIM domains. We demonstrate that such conformational flexibility is necessary for binding of LMO2 to its partner protein SCL/TAL1 in vitro and for the function of this complex in vivo. These results, together with molecular docking and analysis of evolutionarily conserved residues, yield the first structural model of the DNA-binding complex containing LMO2, LDB1, SCL/TAL1, and GATA-1.


    Organizational Affiliation

    Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RHOMBOTIN-2
A
131Homo sapiensMutation(s): 0 
Gene Names: LMO2 (RBTN2, RBTNL1, RHOM2, TTG2)
Find proteins for P25791 (Homo sapiens)
Go to Gene View: LMO2
Go to UniProtKB:  P25791
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
LIM DOMAIN-BINDING PROTEIN 1
B
35Homo sapiensMutation(s): 0 
Gene Names: LDB1 (CLIM2)
Find proteins for Q86U70 (Homo sapiens)
Go to Gene View: LDB1
Go to UniProtKB:  Q86U70
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 25.140α = 90.00
b = 54.360β = 95.45
c = 61.800γ = 90.00
Software Package:
Software NamePurpose
xia2data reduction
BUSTERrefinement
xia2data scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-07-21
    Type: Initial release
  • Version 1.1: 2011-05-19
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance