Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 14.34 kDa 
• Atom Count: 818 
• Modelled Residue Count: 98 
• Deposited Residue Count: 124 
• Unique protein chains: 2

1YCR

MDM2 BOUND TO THE TRANSACTIVATION DOMAIN OF P53

• PDB DOI: 10.2210/pdb1YCR/pdb

• Classification: COMPLEX (ONCOGENE PROTEIN/PEPTIDE)
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1996-09-30 Released: 1997-11-19 
• Deposition Author(s): Kussie, P.H., Pavletich, N.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.276 
• R-Value Work: 0.200 
• R-Value Observed: 0.200 

Literature

Structure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain.

Kussie, P.H., Gorina, S., Marechal, V., Elenbaas, B., Moreau, J., Levine, A.J., Pavletich, N.P.

(1996) Science 274: 948-953

• PubMed: 8875929 
• DOI: 10.1126/science.274.5289.948
• Primary Citation of Related Structures:  
  1YCQ, 1YCR


• PubMed Abstract: 
  

The MDM2 oncoprotein is a cellular inhibitor of the p53 tumor suppressor in that it can bind the transactivation domain of p53 and downregulate its ability to activate transcription. In certain cancers, MDM2 amplification is a common event and contributes to the inactivation of p53. The crystal structure of the 109-residue amino-terminal domain of MDM2 bound to a 15-residue transactivation domain peptide of p53 revealed that MDM2 has a deep hydrophobic cleft on which the p53 peptide binds as an amphipathic alpha helix. The interface relies on the steric complementarity between the MDM2 cleft and the hydrophobic face of the p53 alpha helix and, in particular, on a triad of p53 amino acids-Phe19, Trp23, and Leu26-which insert deep into the MDM2 cleft. These same p53 residues are also involved in transactivation, supporting the hypothesis that MDM2 inactivates p53 by concealing its transactivation domain. The structure also suggests that the amphipathic alpha helix may be a common structural motif in the binding of a diverse family of transactivation factors to the TATA-binding protein-associated factors.

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Organizational Affiliation: 

Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MDM2	A	109	Homo sapiens	Mutation(s): 0  Gene Names: MDM2 EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q00987 (Homo sapiens) Explore Q00987  Go to UniProtKB:  Q00987
PHAROS:  Q00987 GTEx:  ENSG00000135679

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
P53	B	15	N/A	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P04637 (Homo sapiens) Explore P04637  Go to UniProtKB:  P04637
PHAROS:  P04637 GTEx:  ENSG00000141510

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.276 
• R-Value Work: 0.200 
• R-Value Observed: 0.200 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.414	α = 90
b = 100.546	β = 90
c = 54.853	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement
TNT	refinement
X-PLOR	model building
HKL	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1996-09-30 
• Released Date: 1997-11-19 
Deposition Author(s): Kussie, P.H., Pavletich, N.P.

Revision History  

• Version 1.0: 1997-11-19
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-07-17
  Changes: Data collection, Other, Refinement description
• Version 1.4: 2019-08-14
  Changes: Data collection