p53 charged core

Experimental Data Snapshot

  • Resolution: 1.67 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Thermodynamic and Evolutionary Coupling between the Native and Amyloid State of Globular Proteins.

Langenberg, T.Gallardo, R.van der Kant, R.Louros, N.Michiels, E.Duran-Romana, R.Houben, B.Cassio, R.Wilkinson, H.Garcia, T.Ulens, C.Van Durme, J.Rousseau, F.Schymkowitz, J.

(2020) Cell Rep 31: 107512-107512

  • DOI: https://doi.org/10.1016/j.celrep.2020.03.076
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The amyloid-like aggregation propensity present in most globular proteins is generally considered to be a secondary side effect resulting from the requirements of protein stability. Here, we demonstrate, however, that mutations in the globular and amyloid state are thermodynamically correlated rather than simply associated. In addition, we show that the standard genetic code couples this structural correlation into a tight evolutionary relationship. We illustrate the extent of this evolutionary entanglement of amyloid propensity and globular protein stability. Suppressing a 600-Ma-conserved amyloidogenic segment in the p53 core domain fold is structurally feasible but requires 7-bp substitutions to concomitantly introduce two aggregation-suppressing and three stabilizing amino acid mutations. We speculate that, rather than being a corollary of protein evolution, it is equally plausible that positive selection for amyloid structure could have been a driver for the emergence of globular protein structure.

  • Organizational Affiliation

    Switch Laboratory, VIB Center for Brain and Disease Research, Herestraat 49, 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000 Leuven, Belgium.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cellular tumor antigen p53248Homo sapiensMutation(s): 5 
Gene Names: TP53P53
UniProt & NIH Common Fund Data Resources
Find proteins for P04637 (Homo sapiens)
Explore P04637 
Go to UniProtKB:  P04637
PHAROS:  P04637
GTEx:  ENSG00000141510 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04637
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.67 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.423α = 90
b = 84.963β = 90
c = 84.85γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Research CouncilBelgium647458
Research Foundation - FlandersBelgiumSBO-60839

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-11
    Type: Initial release
  • Version 1.1: 2020-09-23
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description