7QI1

Crystal structure of human 14-3-3 protein beta in complex with CFTR peptide pS753pS768 and PPI stabilizer CY007424


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Macrocycle-stabilization of its interaction with 14-3-3 increases plasma membrane localization and activity of CFTR.

Stevers, L.M.Wolter, M.Carlile, G.W.Macdonald, D.Richard, L.Gielkens, F.Hanrahan, J.W.Thomas, D.Y.Chakka, S.K.Peterson, M.L.Thomas, H.Brunsveld, L.Ottmann, C.

(2022) Nat Commun 13: 3586-3586

  • DOI: https://doi.org/10.1038/s41467-022-31206-6
  • Primary Citation of Related Structures:  
    7QI1

  • PubMed Abstract: 

    Impaired activity of the chloride channel CFTR is the cause of cystic fibrosis. 14-3-3 proteins have been shown to stabilize CFTR and increase its biogenesis and activity. Here, we report the identification and mechanism of action of a macrocycle stabilizing the 14-3-3/CFTR complex. This molecule rescues plasma membrane localization and chloride transport of F508del-CFTR and works additively with the CFTR pharmacological chaperone corrector lumacaftor (VX-809) and the triple combination Trikafta®. This macrocycle is a useful tool to study the CFTR/14-3-3 interaction and the potential of molecular glues in cystic fibrosis therapeutics.


  • Organizational Affiliation

    Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
14-3-3 protein thetaA,
B,
E [auth C],
F [auth D]
237Homo sapiensMutation(s): 0 
Gene Names: YWHAQ
UniProt
Find proteins for S7N159 (Myotis brandtii)
Explore S7N159 
Go to UniProtKB:  S7N159
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupS7N159
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cystic fibrosis transmembrane conductance regulatorC [auth F],
D [auth E]
28Homo sapiensMutation(s): 0 
EC: 3.6.3.49 (PDB Primary Data), 5.6.1.6 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P13569 (Homo sapiens)
Explore P13569 
Go to UniProtKB:  P13569
PHAROS:  P13569
GTEx:  ENSG00000001626 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13569
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Q95 (Subject of Investigation/LOI)
Query on Q95

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A]
[2-(2-methylphenyl)sulfanylphenyl]methanamine
C14 H15 N S
CGBSXMIZWLICSP-UHFFFAOYSA-N
TYR
Query on TYR

Download Ideal Coordinates CCD File 
K [auth F],
N [auth C]
TYROSINE
C9 H11 N O3
OUYCCCASQSFEME-QMMMGPOBSA-N
ARG
Query on ARG

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B]
ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O
GLN
Query on GLN

Download Ideal Coordinates CCD File 
L [auth C],
M [auth C]
GLUTAMINE
C5 H10 N2 O3
ZDXPYRJPNDTMRX-VKHMYHEASA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
C [auth F],
D [auth E]
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.367α = 90
b = 111.46β = 90
c = 130.41γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
BUSTERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Netherlands Organisation for Scientific Research (NWO)Netherlands024.001.035

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-25
    Type: Initial release
  • Version 1.1: 2022-07-06
    Changes: Database references
  • Version 1.2: 2022-10-26
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.3: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary