6R4R

Cryo-EM Structure of the PI3-Kinase SH3 Domain Amyloid Fibril


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.4 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Atomic structure of PI3-kinase SH3 amyloid fibrils by cryo-electron microscopy.

Roder, C.Vettore, N.Mangels, L.N.Gremer, L.Ravelli, R.B.G.Willbold, D.Hoyer, W.Buell, A.K.Schroder, G.F.

(2019) Nat Commun 10: 3754-3754

  • DOI: 10.1038/s41467-019-11320-8

  • PubMed Abstract: 
  • High resolution structural information on amyloid fibrils is crucial for the understanding of their formation mechanisms and for the rational design of amyloid inhibitors in the context of protein misfolding diseases. The Src-homology 3 domain of pho ...

    High resolution structural information on amyloid fibrils is crucial for the understanding of their formation mechanisms and for the rational design of amyloid inhibitors in the context of protein misfolding diseases. The Src-homology 3 domain of phosphatidyl-inositol-3-kinase (PI3K-SH3) is a model amyloid system that plays a pivotal role in our basic understanding of protein misfolding and aggregation. Here, we present the atomic model of the PI3K-SH3 amyloid fibril with a resolution determined to 3.4 Å by cryo-electron microscopy (cryo-EM). The fibril is composed of two intertwined protofilaments that create an interface spanning 13 residues from each monomer. The model comprises residues 1-77 out of 86 amino acids in total, with the missing residues located in the highly flexible C-terminus. The fibril structure allows us to rationalise the effects of chemically conservative point mutations as well as of the previously reported sequence perturbations on PI3K-SH3 fibril formation and growth.


    Organizational Affiliation

    Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany.,Physics Department, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany. gu.schroeder@fz-juelich.de.,Institute of Complex Systems, Structural Biochemistry (ICS-6) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425, Jülich, Germany. gu.schroeder@fz-juelich.de.,The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany. alebu@dtu.dk.,Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kgs, Lyngby, Denmark. alebu@dtu.dk.,Institute of Complex Systems, Structural Biochemistry (ICS-6) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425, Jülich, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphatidylinositol 3-kinase regulatory subunit alpha
A, B, C, D, E, F, G
86Bos taurusMutation(s): 0 
Gene Names: PIK3R1
Find proteins for P23727 (Bos taurus)
Go to Gene View: PIK3R1
Go to UniProtKB:  P23727
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.4 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European CommissionGermany726368
German Research FoundationGermanySFB 974
German Research FoundationGermanySFB 1208
German Research FoundationGermany--

Revision History 

  • Version 1.0: 2019-08-28
    Type: Initial release
  • Version 1.1: 2019-09-04
    Type: Data collection, Database references