NMR structure of unliganded MDM2

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 110 
  • Conformers Submitted: 24 
  • Selection Criteria: structures with favorable non-bond energy 

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Structure of Free MDM2 N-terminal Domain Reveals Conformational Adjustments that Accompany p53-binding

Uhrinova, S.Uhrin, D.Powers, H.Watt, K.Zheleva, D.Fischer, P.McInnes, C.Barlow, P.N.

(2005) J Mol Biol 350: 587-598

  • DOI: https://doi.org/10.1016/j.jmb.2005.05.010
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Critical to the inhibitory action of the oncogene product, MDM2, on the tumour suppressor, p53, is association of the N-terminal domain of MDM2 (MDM2N) with the transactivation domain of p53. The structure of MDM2N was previously solved with a p53-derived peptide, or small-molecule ligands, occupying its binding cleft, but no structure of the non-liganded MDM2N (i.e. the apo-form) has been reported. Here, we describe the solution structure and dynamics of apo-MDM2N and thus reveal the nature of the conformational changes in MDM2N that accompany binding of p53. The new structure suggests that p53 effects displacement of an N-terminal segment of apo-MDM2N that occludes access to the shallow end of the p53-binding cleft. MDM2N must also undergo an expansion upon binding, achieved through a rearrangement of its two pseudosymetrically related sub-domains resulting in outward displacements of the secondary structural elements that comprise the walls and floor of the p53-binding cleft. MDM2N becomes more rigid and stable upon binding p53. Conformational plasticity of the binding cleft of apo-MDM2N could allow the parent protein to bind specifically to several different partners, although, to date, all the known liganded structures of MDM2N are highly similar to one another. The results indicate that the more open conformation of the binding cleft of MDM2N observed in structures of complexes with small molecules and peptides is a more suitable one for ligand discovery and optimisation.

  • Organizational Affiliation

    Schools of Chemistry and Biological Sciences, University of Edinburgh, King's Buildings, West Mains Road, Edinburgh EH9 3JR, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-protein ligase E3 Mdm2119Homo sapiensMutation(s): 0 
EC: 6.3.2
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Find proteins for Q00987 (Homo sapiens)
Explore Q00987 
Go to UniProtKB:  Q00987
PHAROS:  Q00987
GTEx:  ENSG00000135679 
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UniProt GroupQ00987
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 110 
  • Conformers Submitted: 24 
  • Selection Criteria: structures with favorable non-bond energy 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-06-28
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-03-02
    Changes: Data collection, Database references, Derived calculations