4FR3 | pdb_00004fr3

Crystal structure of human 14-3-3 sigma in complex with TASK-3 peptide and stabilizer 16-O-Me-FC-H


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.209 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.168 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.170 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 0V4Click on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

A semisynthetic fusicoccane stabilizes a protein-protein interaction and enhances the expression of k(+) channels at the cell surface.

Anders, C.Higuchi, Y.Koschinsky, K.Bartel, M.Schumacher, B.Thiel, P.Nitta, H.Preisig-Muller, R.Schlichthorl, G.Renigunta, V.Ohkanda, J.Daut, J.Kato, N.Ottmann, C.

(2013) Chem Biol 20: 583-593

  • DOI: https://doi.org/10.1016/j.chembiol.2013.03.015
  • Primary Citation of Related Structures:  
    3P1N, 3P1O, 3P1P, 3P1Q, 3P1R, 3P1S, 3SMK, 3SML, 3SMM, 3SMN, 3SMO, 3SP5, 3SPR, 3UX0, 4FR3

  • PubMed Abstract: 

    Small-molecule stabilization of protein-protein interactions is an emerging field in chemical biology. We show how fusicoccanes, originally identified as fungal toxins acting on plants, promote the interaction of 14-3-3 proteins with the human potassium channel TASK-3 and present a semisynthetic fusicoccane derivative (FC-THF) that targets the 14-3-3 recognition motif (mode 3) in TASK-3. In the presence of FC-THF, the binding of 14-3-3 proteins to TASK-3 was increased 19-fold and protein crystallography provided the atomic details of the effects of FC-THF on this interaction. We also tested the functional effects of FC-THF on TASK channels heterologously expressed in Xenopus oocytes. Incubation with 10 μM FC-THF was found to promote the transport of TASK channels to the cell membrane, leading to a significantly higher density of channels at the surface membrane and increased potassium current.


  • Organizational Affiliation

    Chemical Genomics Centre of the Max-Planck-Society, 44227 Dortmund, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
14-3-3 protein sigma234Homo sapiensMutation(s): 0 
Gene Names: HME1SFN
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
TASK-3 peptideB [auth P]6Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NPC2 (Homo sapiens)
Explore Q9NPC2 
Go to UniProtKB:  Q9NPC2
PHAROS:  Q9NPC2
GTEx:  ENSG00000169427 
Entity Groups  
UniProt GroupQ9NPC2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0V4
Query on 0V4

Download Ideal Coordinates CCD File 
C [auth A](4R,5R,6R,6aS,9S,9aE,10aR)-5-hydroxy-9-(methoxymethyl)-6,10a-dimethyl-3-(propan-2-yl)-1,2,4,5,6,6a,7,8,9,10a-decahydrodicyclopenta[a,d][8]annulen-4-yl alpha-D-glucopyranoside
C27 H44 O8
ZKINNMSFCCOPQI-MKYFCGQTSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
SEP
Query on SEP
B [auth P]L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.209 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.168 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.170 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.68α = 90
b = 111.99β = 90
c = 62.97γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 0V4Click on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-08
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Advisory, Refinement description
  • Version 1.2: 2023-09-13
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-12-06
    Changes: Data collection
  • Version 1.4: 2024-11-20
    Changes: Structure summary