9F35 | pdb_00009f35

Co-crystal structure of 14-3-3sigma in complex with B-Raf pS365 phosphopeptide

  • Classification: PEPTIDE BINDING PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2024-04-24 Released: 2025-02-05 
  • Deposition Author(s): Wu, Q.
  • Funding Organization(s): European Union (EU), Netherlands Organisation for Scientific Research (NWO), Other government

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.298 (Depositor), 0.295 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.213 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Proximity-enhanced cysteine-histidine crosslinking for elucidating intrinsically disordered and other protein complexes.

Wu, Q.van den Wildenberg, S.A.H.Brzoskowski, J.C.R.van den Oetelaar, M.C.M.Verhoef, C.J.A.Genet, S.A.A.M.Ottmann, C.Markvoort, A.J.Brunsveld, L.Cossar, P.J.

(2025) Chem Sci 16: 3523-3535

  • DOI: https://doi.org/10.1039/d4sc07419j
  • Primary Citation of Related Structures:  
    9F35

  • PubMed Abstract: 

    Disordered proteins and domains are ubiquitous throughout the proteome of human cell types, yet the biomolecular sciences lack effective tool compounds and chemical strategies to study this class of proteins. In this context, we introduce a novel covalent tool compound approach that combines proximity-enhanced crosslinking with histidine trapping. Utilizing a maleimide-cyclohexenone crosslinker for efficient cysteine-histidine crosslinking, we elucidated the mechanism of this dual-reactive tool compound class. This tool compound concept was then applied to profile the full-length complex of 14-3-3 and hyperphosphorylated Tau (hpTau), relevant to Alzheimer's. This approach identified a cryptic binding interaction between 14-3-3 and hpTau via its phosphorylated Ser356, overlooked by the majority of 14-3-3/Tau literature. Utilizing a mutational study and an equilibrium model, this cryptic binding interaction is revealed to play a prominent biomolecular role at cellularly relevant concentrations. This finding necessitates a re-evaluation of the mechanism of the 14-3-3/Tau interaction. The histidine-trap crosslinker approach reported here not only advances our understanding of the 14-3-3/Tau interaction but also demonstrates the potential of dual-covalent tool compounds in studying complex interactions involving IDPs and IDDs.


  • Organizational Affiliation

    Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology Netherlands l.brunsveld@tue.nl p.cossar@tue.nl.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
14-3-3 protein sigma236Homo sapiensMutation(s): 0 
Gene Names: SFNHME1
UniProt & NIH Common Fund Data Resources
Find proteins for P31947 (Homo sapiens)
Explore P31947 
Go to UniProtKB:  P31947
PHAROS:  P31947
GTEx:  ENSG00000175793 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31947
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase B-raf11Homo sapiensMutation(s): 0 
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P15056 (Homo sapiens)
Explore P15056 
Go to UniProtKB:  P15056
PHAROS:  P15056
GTEx:  ENSG00000157764 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15056
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
SEP
Query on SEP
B
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.298 (Depositor), 0.295 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.213 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.782α = 90
b = 115.252β = 90
c = 64.671γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
Cootmodel building
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2025-02-05 
  • Deposition Author(s): Wu, Q.

Funding OrganizationLocationGrant Number
European Union (EU)European Union101098234
Netherlands Organisation for Scientific Research (NWO)NetherlandsVI.Veni.212.27
Other governmentChinaCSC 201906050031

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-05
    Type: Initial release
  • Version 1.1: 2025-03-05
    Changes: Database references