7QI1 | pdb_00007qi1

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

• PDB DOI: https://doi.org/10.2210/pdb7QI1/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-12-14 Released: 2022-05-25 
• Deposition Author(s): Stevers, L.M., Ottmann, C.
• Funding Organization(s): Netherlands Organisation for Scientific Research (NWO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.241 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.195 (Depositor) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

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

• PubMed: 35739107 
• DOI: https://doi.org/10.1038/s41467-022-31206-6
• Primary Citation 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.

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Organizational Affiliation: 
• Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands.
Cystic Fibrosis Translational Research Centre, Department of Biochemistry and Physiology, McGill University, Montreal, QC, Canada.
Cyclenium Pharma Inc., 7171 rue Frederick Banting, Montreal, Quebec, Canada.
Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A4B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - A4 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 116.44 kDa 
• Atom Count: 8,367 
• Modeled Residue Count: 971 
• Deposited Residue Count: 1,004 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
14-3-3 protein theta	A, B, E [auth C], F [auth D]	237	Homo sapiens	Mutation(s): 0  Gene Names: YWHAQ
UniProt
Find proteins for S7N159 (Myotis brandtii) Explore S7N159  Go to UniProtKB:  S7N159

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cystic fibrosis transmembrane conductance regulator	C [auth F], D [auth E]	28	Homo sapiens	Mutation(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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Q95 (Subject of Investigation/LOI)	H [auth A], I [auth A]	[2-(2-methylphenyl)sulfanylphenyl]methanamine C14 H15 N S CGBSXMIZWLICSP-UHFFFAOYSA-N
TYR	K [auth F], N [auth C]	TYROSINE C9 H11 N O3 OUYCCCASQSFEME-QMMMGPOBSA-N
ARG	G [auth A], J [auth B]	ARGININE C6 H15 N4 O2 ODKSFYDXXFIFQN-BYPYZUCNSA-O
GLN	L [auth C], M [auth C]	GLUTAMINE C5 H10 N2 O3 ZDXPYRJPNDTMRX-VKHMYHEASA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	C [auth F], D [auth E]	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.241 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.195 (Depositor) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.367	α = 90
b = 111.46	β = 90
c = 130.41	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
BUSTER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-05-25 
Deposition Author(s): Stevers, L.M., Ottmann, C.

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Funding Organization	Location	Grant Number
Netherlands Organisation for Scientific Research (NWO)	Netherlands	024.001.035

Revision History  

• 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