2LP5 | pdb_00002lp5

Native Structure of the Fyn SH3 A39V/N53P/V55L


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 1000 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

Validation slider image for 2LP5

This is version 1.2 of the entry. See complete history

Literature

Structure of an intermediate state in protein folding and aggregation.

Neudecker, P.Robustelli, P.Cavalli, A.Walsh, P.Lundstrom, P.Zarrine-Afsar, A.Sharpe, S.Vendruscolo, M.Kay, L.E.

(2012) Science 336: 362-366

  • DOI: https://doi.org/10.1126/science.1214203
  • Primary Citation Related Structures: 
    2L2P, 2LP5

  • PubMed Abstract: 

    Protein-folding intermediates have been implicated in amyloid fibril formation involved in neurodegenerative disorders. However, the structural mechanisms by which intermediates initiate fibrillar aggregation have remained largely elusive. To gain insight, we used relaxation dispersion nuclear magnetic resonance spectroscopy to determine the structure of a low-populated, on-pathway folding intermediate of the A39V/N53P/V55L (A, Ala; V, Val; N, Asn; P, Pro; L, Leu) Fyn SH3 domain. The carboxyl terminus remains disordered in this intermediate, thereby exposing the aggregation-prone amino-terminal β strand. Accordingly, mutants lacking the carboxyl terminus and thus mimicking the intermediate fail to safeguard the folding route and spontaneously form fibrillar aggregates. The structure provides a detailed characterization of the non-native interactions stabilizing an aggregation-prone intermediate under native conditions and insight into how such an intermediate can derail folding and initiate fibrillation.


  • Organizational Affiliation
    • Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada.

Macromolecule Content 

  • Total Structure Weight: 7.54 kDa 
  • Atom Count: 480 
  • Modeled Residue Count: 59 
  • Deposited Residue Count: 66 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase Fyn66Gallus gallusMutation(s): 3 
Gene Names: FYN
EC: 2.7.10.2
UniProt
Find proteins for Q05876 (Gallus gallus)
Explore Q05876 
Go to UniProtKB:  Q05876
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05876
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 1000 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-16
    Type: Initial release
  • Version 1.1: 2023-06-14
    Changes: Advisory, Data collection, Database references, Other
  • Version 1.2: 2024-05-15
    Changes: Data collection, Database references