7ZMU | pdb_00007zmu

14-3-3s binding to non-natural peptide 2d

• PDB DOI: https://doi.org/10.2210/pdb7ZMU/pdb

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


• Deposited: 2022-04-19 Released: 2022-11-23 
• Deposition Author(s): Somsen, B.A., Craenmehr, F.W.B., Ottmann, C.
• Funding Organization(s): Netherlands Organisation for Scientific Research (NWO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.294 (Depositor), 0.294 (DCC) 
• R-Value Work: 
  0.254 (Depositor), 0.254 (DCC) 
• R-Value Observed: 
  0.256 (Depositor) 

Starting Model: experimental

Literature

Functional mapping of the 14-3-3 hub protein as a guide to design 14-3-3 molecular glues.

Somsen, B.A., Craenmehr, F.W.B., Liu, W.W., Koops, A.A., Pennings, M.A.M., Visser, E.J., Ottmann, C., Cossar, P.J., Brunsveld, L.

(2022) Chem Sci 13: 13122-13131

• PubMed: 36425501 
• DOI: https://doi.org/10.1039/d2sc04662h
• Primary Citation Related Structures: 
  7ZMU, 7ZMW


• PubMed Abstract: 
  

  Molecular glues represent an evolution in drug discovery, however, targeted stabilization of protein complexes remains challenging, owing to a paucity of drug design rules. The functional mapping of hotspots has been critical to protein-protein interaction (PPI) inhibitor research, however, the orthogonal approach to stabilize PPIs has not exploited this information. Utilizing the hub protein 14-3-3 as a case study we demonstrate that functional mapping of hotspots provides a triage map for 14-3-3 molecular glue development. Truncation and mutation studies allowed deconvoluting the energetic contributions of sidechain and backbone interactions of a 14-3-3-binding non-natural peptide. Three central 14-3-3 hotspots were identified and their thermodynamic characteristics profiled. In addition to the phospho-binding pocket; (i) Asn226, (ii) Lys122 and (iii) the hydrophobic patch formed by Leu218, Ile219 and Leu222 were critical for protein complex formation. Exploiting this hotspot information allowed a peptide-based molecular glue that elicits high cooperativity ( α = 36) and selectively stabilizes the 14-3-3/ChREBP PPI to be uniquely developed.

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Organizational Affiliation: 
• Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology P.O. Box 513 Eindhoven 5600 MB The Netherlands [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Macromolecule Content 

• Total Structure Weight: 27.46 kDa 
• Atom Count: 2,230 
• Modeled Residue Count: 243 
• Deposited Residue Count: 243 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
14-3-3 protein sigma	A	236	Homo sapiens	Mutation(s): 0  Gene Names: SFN, HME1
UniProt & NIH Common Fund Data Resources
Find proteins for P31947 (Homo sapiens) Explore P31947  Go to UniProtKB:  P31947
PHAROS:  P31947 GTEx:  ENSG00000175793

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
non-natural peptide 2	B	7	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
B3S	B	D-PEPTIDE LINKING	C4 H9 N O3		--
BAL	B	PEPTIDE-LIKE	C3 H7 N O2		--
PPN	B	L-PEPTIDE LINKING	C9 H10 N2 O4		PHE
SEP	B	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.294 (Depositor), 0.294 (DCC) 
• R-Value Work:  0.254 (Depositor), 0.254 (DCC) 
• R-Value Observed: 0.256 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.278	α = 90
b = 112.007	β = 90
c = 62.68	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
Coot	model building
Aimless	data scaling
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-11-23 
Deposition Author(s): Somsen, B.A., Craenmehr, F.W.B., Ottmann, C.

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Funding Organization	Location	Grant Number
Netherlands Organisation for Scientific Research (NWO)	Netherlands	711.017.014

Revision History  

• Version 1.0: 2022-11-23
  Type: Initial release
  
• Version 1.1: 2022-12-07
  Changes: Database references
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection
• Version 2.1: 2024-01-31
  Changes: Refinement description