4KFZ

Crystal structure of LMO2 and anti-LMO2 VH complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.240 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Conformational flexibility of the oncogenic protein LMO2 primes the formation of the multi-protein transcription complex.

Sewell, H.Tanaka, T.Omari, K.E.Mancini, E.J.Cruz, A.Fernandez-Fuentes, N.Chambers, J.Rabbitts, T.H.

(2014) Sci Rep 4: 3643-3643

  • DOI: https://doi.org/10.1038/srep03643
  • Primary Citation of Related Structures:  
    4KFZ

  • PubMed Abstract: 

    LMO2 was discovered via chromosomal translocations in T-cell leukaemia and shown normally to be essential for haematopoiesis. LMO2 is made up of two LIM only domains (thus it is a LIM-only protein) and forms a bridge in a multi-protein complex. We have studied the mechanism of formation of this complex using a single domain antibody fragment that inhibits LMO2 by sequestering it in a non-functional form. The crystal structure of LMO2 with this antibody fragment has been solved revealing a conformational difference in the positioning and angle between the two LIM domains compared with its normal binding. This contortion occurs by bending at a central helical region of LMO2. This is a unique mechanism for inhibiting an intracellular protein function and the structural contusion implies a model in which newly synthesized, intrinsically disordered LMO2 binds to a partner protein nucleating further interactions and suggests approaches for therapeutic targeting of LMO2.


  • Organizational Affiliation

    1] Weatherall Institute of Molecular Medicine MRC Molecular Haematology Unit University of Oxford John Radcliffe Hospital Oxford OX3 9DS, UK [2] Leeds Institute of Molecular Medicine Wellcome Trust Brenner Building St. James's University Hospital University of Leeds Leeds, LS9 7TF, UK [3] [4].


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LMO-2
A, B
150Homo sapiensMutation(s): 0 
Gene Names: LMO2RBTN2RBTNL1RHOM2TTG2
UniProt & NIH Common Fund Data Resources
Find proteins for P25791 (Homo sapiens)
Explore P25791 
Go to UniProtKB:  P25791
PHAROS:  P25791
GTEx:  ENSG00000135363 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25791
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Anti-LMO2 VH
C, D
129Homo sapiensMutation(s): 0 
Gene Names: Anti-LMO2 VH
UniProt & NIH Common Fund Data Resources
Find proteins for P01764 (Homo sapiens)
Explore P01764 
Go to UniProtKB:  P01764
PHAROS:  P01764
GTEx:  ENSG00000211949 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01764
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.240 
  • Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.26α = 90
b = 124.26β = 90
c = 81.44γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-22
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description