Biological Assembly 1  

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

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Macromolecule Content

• Total Structure Weight: 30.18 kDa 
• Atom Count: 1850 
• Modelled Residue Count: 214 
• Deposited Residue Count: 266 
• Unique protein chains: 2

4UMN

Structure of a stapled peptide antagonist bound to Nutlin-resistant Mdm2.

• PDB DOI: 10.2210/pdb4UMN/pdb

• Classification: CELL CYCLE
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-05-20 Released: 2014-05-28 
• Deposition Author(s): Chee, S., Wongsantichon, J., Quah, S., Robinson, R.C., Verma, C., Lane, D.P., Brown, C.J., Ghadessy, F.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 0.237 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 

Literature

Structure of a stapled peptide antagonist bound to nutlin-resistant Mdm2.

Chee, S.M., Wongsantichon, J., Soo Tng, Q., Robinson, R., Joseph, T.L., Verma, C., Lane, D.P., Brown, C.J., Ghadessy, F.J.

(2014) PLoS One 9: e104914-e104914

• PubMed: 25115702 
• DOI: 10.1371/journal.pone.0104914
• Primary Citation of Related Structures:  
  4UMN


• PubMed Abstract: 
  

As key negative regulator of the p53 tumour suppressor, Mdm2 is an attractive therapeutic target. Small molecules such as Nutlin have been developed to antagonise Mdm2, resulting in p53-dependent death of tumour cells. We have recently described a mutation in Mdm2 (M62A), which precludes binding of Nutlin, but not p53. This Nutlin-resistant variant is not, however, refractory to binding and inhibition by stapled peptide antagonists targeting the same region of Mdm2. A detailed understanding of how stapled peptides are recalcitrant to Mdm2 mutations conferring Nutlin-resistance will aid in the further development of potent Mdm2 antagonists. Here, we report the 2.00 Å crystal structure of a stapled peptide antagonist bound to Nutlin resistant Mdm2. The stapled peptide relies on an extended network of interactions along the hydrophobic binding cleft of Mdm2 for high affinity binding. Additionally, as seen in other stapled peptide structures, the hydrocarbon staple itself contributes to binding through favourable interactions with Mdm2. The structure highlights the intrinsic plasticity present in both Mdm2 and the hydrocarbon staple moiety, and can be used to guide future iterations of both small molecules and stapled peptides for improved antagonists of Mdm2.

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Organizational Affiliation: 

p53Lab, Agency for Science Technology and Research (A*STAR), Singapore, Singapore.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 UBIQUITIN-PROTEIN LIGASE MDM2	A, B	120	Homo sapiens	Mutation(s): 1  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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
M06	C, D	13	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MK8	C, D	L-PEPTIDE LINKING	C7 H15 N O2		LEU

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 0.237 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.076	α = 90
b = 65.674	β = 90
c = 105.683	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-05-20 
• Released Date: 2014-05-28 
Deposition Author(s): Chee, S., Wongsantichon, J., Quah, S., Robinson, R.C., Verma, C., Lane, D.P., Brown, C.J., Ghadessy, F.J.

Revision History  

• Version 1.0: 2014-05-28
  Type: Initial release
  
• Version 1.1: 2014-07-16
  Changes: Atomic model, Other
• Version 1.2: 2014-08-27
  Changes: Database references
• Version 1.3: 2017-08-09
  Changes: Database references
• Version 1.4: 2019-10-16
  Changes: Data collection, Derived calculations, Experimental preparation, Other