5SWK

Crystal structure of p53 epitope-scaffold based on a inhibitor of cysteine proteases in complex with human MDM2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.923 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Mimicking a p53-MDM2 interaction based on a stable immunoglobulin-like domain scaffold.

Jimenez-Sandoval, P.Madrigal-Carrillo, E.A.Santamaria-Suarez, H.A.Maturana, D.Renteria-Gonzalez, I.Benitez-Cardoza, C.G.Torres-Larios, A.Brieba, L.G.

(2018) Proteins 86: 802-812

  • DOI: 10.1002/prot.25519

  • PubMed Abstract: 
  • Antibodies recognize protein targets with great affinity and specificity. However, posttranslational modifications and the presence of intrinsic disulfide-bonds pose difficulties for their industrial use. The immunoglobulin fold is one of the most ub ...

    Antibodies recognize protein targets with great affinity and specificity. However, posttranslational modifications and the presence of intrinsic disulfide-bonds pose difficulties for their industrial use. The immunoglobulin fold is one of the most ubiquitous folds in nature and it is found in many proteins besides antibodies. An example of a protein family with an immunoglobulin-like fold is the Cysteine Protease Inhibitors (ICP) family I42 of the MEROPs database for protease and protease inhibitors. Members of this protein family are thermostable and do not present internal disulfide bonds. Crystal structures of several ICPs indicate that they resemble the Ig-like domain of the human T cell co-receptor CD8α As ICPs present 2 flexible recognition loops that vary accordingly to their targeted protease, we hypothesize that members of this protein family would be ideal to design peptide aptamers that mimic protein-protein interactions. Herein, we use an ICP variant from Entamoeba histolytica (EhICP1) to mimic the interaction between p53 and MDM2. We found that a 13 amino-acid peptide derived from p53 can be introduced in 2 variable loops (DE, FG) but not the third (BC). Chimeric EhICP1-p53 form a stable complex with MDM2 at a micromolar range. Crystal structure of the EhICP1-p53(FG)-loop variant in complex with MDM2 reveals a swapping subdomain between 2 chimeric molecules, however, the p53 peptide interacts with MDM2 as in previous crystal structures. The structural details of the EhICP1-p53(FG) interaction with MDM2 resemble the interaction between an antibody and MDM2.


    Organizational Affiliation

    Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Irapuato, Guanajuato, CP 36821, México.,NanoTemper Technologies GmbH, Floessergasse 4, Munich, 81369, Germany.,Laboratorio de Investigación Bioquímica, Programa Institucional en Biomedicina Molecular ENMyH-Instituto Politécnico Nacional, Guillermo Massieu Helguera No. 239, La Escalera Ticoman, D.F, Mexico City, 07320, Mexico.,Departamento de Bioquímica y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Apartado Postal 70-243, Mexico City, 04510, México.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase Mdm2
A, B
153Homo sapiensMutation(s): 0 
Gene Names: MDM2
EC: 2.3.2.27
Find proteins for Q00987 (Homo sapiens)
Go to Gene View: MDM2
Go to UniProtKB:  Q00987
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
De novo protein based on the inhibitor Amoebiasin-1
C, D
110N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.923 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.221 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 87.361α = 90.00
b = 87.361β = 90.00
c = 160.840γ = 90.00
Software Package:
Software NamePurpose
iMOSFLMdata processing
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
Cootmodel building
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
CONACyTMexicoFronteras de la ciencia No. 11

Revision History 

  • Version 1.0: 2017-10-18
    Type: Initial release
  • Version 1.1: 2019-05-01
    Type: Data collection, Database references