3EQY

Crystal structure of human MDMX in complex with a 12-mer peptide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for high-affinity peptide inhibition of p53 interactions with MDM2 and MDMX.

Pazgier, M.Liu, M.Zou, G.Yuan, W.Li, C.Li, C.Li, J.Monbo, J.Zella, D.Tarasov, S.G.Lu, W.

(2009) Proc.Natl.Acad.Sci.USA 106: 4665-4670

  • DOI: 10.1073/pnas.0900947106
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The oncoproteins MDM2 and MDMX negatively regulate the activity and stability of the tumor suppressor protein p53--a cellular process initiated by MDM2 and/or MDMX binding to the N-terminal transactivation domain of p53. MDM2 and MDMX in many tumors ...

    The oncoproteins MDM2 and MDMX negatively regulate the activity and stability of the tumor suppressor protein p53--a cellular process initiated by MDM2 and/or MDMX binding to the N-terminal transactivation domain of p53. MDM2 and MDMX in many tumors confer p53 inactivation and tumor survival, and are important molecular targets for anticancer therapy. We screened a duodecimal peptide phage library against site-specifically biotinylated p53-binding domains of human MDM2 and MDMX chemically synthesized via native chemical ligation, and identified several peptide inhibitors of the p53-MDM2/MDMX interactions. The most potent inhibitor (TSFAEYWNLLSP), termed PMI, bound to MDM2 and MDMX at low nanomolar affinities--approximately 2 orders of magnitude stronger than the wild-type p53 peptide of the same length (ETFSDLWKLLPE). We solved the crystal structures of synthetic MDM2 and MDMX, both in complex with PMI, at 1.6 A resolution. Comparative structural analysis identified an extensive, tightened intramolecular H-bonding network in bound PMI that contributed to its conformational stability, thus enhanced binding to the 2 oncogenic proteins. Importantly, the C-terminal residue Pro of PMI induced formation of a hydrophobic cleft in MDMX previously unseen in the structures of p53-bound MDM2 or MDMX. Our findings deciphered the structural basis for high-affinity peptide inhibition of p53 interactions with MDM2 and MDMX, shedding new light on structure-based rational design of different classes of p53 activators for potential therapeutic use.


    Organizational Affiliation

    Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mdm4 protein
A, B
85Homo sapiensMutation(s): 3 
Gene Names: MDM4 (MDMX)
Find proteins for O15151 (Homo sapiens)
Go to Gene View: MDM4
Go to UniProtKB:  O15151
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
12-mer peptide inhibitor
C, D
12N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GAI
Query on GAI

Download SDF File 
Download CCD File 
A, B
GUANIDINE
C H5 N3
ZRALSGWEFCBTJO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.155 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 75.627α = 90.00
b = 75.627β = 90.00
c = 35.181γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
PHASERphasing
SCALEPACKdata scaling
REFMACrefinement
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-10-01 
  • Released Date: 2009-03-17 
  • Deposition Author(s): Pazgier, M., Lu, W.

Revision History 

  • Version 1.0: 2009-03-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2014-04-02
    Type: Source and taxonomy