6FAV | pdb_00006fav

Crystal structure of C-terminal modified Tau peptide-hybrid 4.2f-I with 14-3-3sigma


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 
    0.171 (Depositor), 0.174 (DCC) 
  • R-Value Work: 
    0.144 (Depositor), 0.147 (DCC) 
  • R-Value Observed: 
    0.146 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Inhibition of 14-3-3/Tau by Hybrid Small-Molecule Peptides Operating via Two Different Binding Modes.

Andrei, S.A.Meijer, F.A.Neves, J.F.Brunsveld, L.Landrieu, I.Ottmann, C.Milroy, L.G.

(2018) ACS Chem Neurosci 9: 2639-2654

  • DOI: https://doi.org/10.1021/acschemneuro.8b00118
  • Primary Citation Related Structures: 
    6FAU, 6FAV, 6FAW, 6FBW, 6FBY, 6FI4, 6FI5

  • PubMed Abstract: 

    Current molecular hypotheses have not yet delivered marketable treatments for Alzheimer's disease (AD), arguably due to a lack of understanding of AD biology and an overreliance on conventional drug modalities. Protein-protein interactions (PPIs) are emerging drug targets, which show promise for the treatment of, e.g., cancer, but are still underexploited for treating neurodegenerative diseases. 14-3-3 binding to phosphorylated Tau is a promising PPI drug target based on its reported destabilizing effect on microtubules, leading to enhanced neurofibrillary tangle formation as a potential cause of AD-related neurodegeneration. Inhibition of 14-3-3/Tau may therefore be neuroprotective. Previously, we reported the structure-guided development of modified peptide inhibitors of 14-3-3/Tau. Here, we report further efforts to optimize the binding mode and activity of our modified Tau peptides through a combination of chemical synthesis, biochemical assays, and X-ray crystallography. Most notably, we were able to characterize two different high-affinity binding modes, both of which inhibited 14-3-3-binding to full-length PKA-phosphorylated Tau protein in vitro as measured by NMR spectroscopy. Our findings, besides producing useful tool inhibitor compounds for studying 14-3-3/Tau, have enhanced our understanding of the molecular parameters for inhibiting 14-3-3/Tau, which are important milestones toward the establishment of our 14-3-3 PPI hypothesis.


  • Organizational Affiliation
    • Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems , Technische Universiteit Eindhoven , Den Dolech 2 , 5612 AZ Eindhoven , The Netherlands.

Macromolecule Content 

  • Total Structure Weight: 55.29 kDa 
  • Atom Count: 4,823 
  • Modeled Residue Count: 471 
  • Deposited Residue Count: 486 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
14-3-3 protein sigma
A, C
236Homo 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
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ACE-ARG-THR-PRO-SEP-LEU-PRO-GLY8Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P10636 (Homo sapiens)
Explore P10636 
Go to UniProtKB:  P10636
PHAROS:  P10636
GTEx:  ENSG00000186868 
Entity Groups
UniProt GroupP10636
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
THR-PRO-SEP-LEU-PRO-GLY6Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P10636 (Homo sapiens)
Explore P10636 
Go to UniProtKB:  P10636
PHAROS:  P10636
GTEx:  ENSG00000186868 
Entity Groups
UniProt GroupP10636
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D3Q
(Subject of Investigation/LOI)

Query on D3Q



Download:Ideal Coordinates CCD File
H [auth B],
M [auth D]
(2~{R})-2-[(~{R})-(3-methoxyphenyl)-phenyl-methyl]pyrrolidine
C18 H21 N O
JABPEOHMWOYYAX-QZTJIDSGSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
I [auth C],
J [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
G [auth A],
K [auth C],
L [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
B
L-PEPTIDE LINKINGC3 H8 N O6 PSER

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free:  0.171 (Depositor), 0.174 (DCC) 
  • R-Value Work:  0.144 (Depositor), 0.147 (DCC) 
  • R-Value Observed: 0.146 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.789α = 90
b = 70.14β = 90
c = 128.259γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Netherlands--

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-16
    Type: Initial release
  • Version 1.1: 2018-11-28
    Changes: Data collection, Database references
  • Version 1.2: 2019-02-27
    Changes: Data collection, Derived calculations
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary