6G8J | pdb_00006g8j

14-3-3sigma in complex with a A130beta3A mutated YAP pS127 phosphopeptide

• PDB DOI: https://doi.org/10.2210/pdb6G8J/pdb

• Classification: ONCOPROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-04-09 Released: 2019-04-17 
• Deposition Author(s): Andrei, S.A., Thijssen, V., Brunsveld, L., Ottmann, C., Milroy, L.G.
• Funding Organization(s): Netherlands Organisation for Scientific Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 
  0.173 (Depositor), 0.174 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

Literature

A study on the effect of synthetic alpha-to-beta3-amino acid mutations on the binding of phosphopeptides to 14-3-3 proteins.

Andrei, S.A., Thijssen, V., Brunsveld, L., Ottmann, C., Milroy, L.G.

(2019) Chem Commun (Camb) 55: 14809-14812

• PubMed: 31763628 
• DOI: https://doi.org/10.1039/c9cc07982c
• Primary Citation Related Structures: 
  6G6X, 6G8I, 6G8J, 6G8K, 6G8L, 6G8P, 6G8Q


• PubMed Abstract: 
  

  Here we describe the synthesis of a series of α,β-phosphopeptides, based on the phosphoepitope site on YAP1 (yes-associated protein 1), and the biochemical, biophysical and structural characterization of their binding to 14-3-3 proteins. The impact of systematic mono- and di-substitution of α → β3 amino acid residues around the phosphoserine residue are discussed. Our results confirm the important role played by the +2 proline residue in the thermodynamics and structure of the phosphoepitope/14-3-3 interaction.

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

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 27.8 kDa 
• Atom Count: 2,525 
• Modeled Residue Count: 242 
• Deposited Residue Count: 247 
• 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
ACE-ARG-ALA-HIS-SEP-SER-PRO-BAL-SER-LEU-GLN	B [auth P]	11	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P46937 (Homo sapiens) Explore P46937  Go to UniProtKB:  P46937
PHAROS:  P46937 GTEx:  ENSG00000137693

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
B3A	B [auth P]	L-PEPTIDE LINKING	C4 H9 N O2		ALA
SEP	B [auth P]	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free:  0.173 (Depositor), 0.174 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.149	α = 90
b = 112.019	β = 90
c = 62.68	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-04-17 
Deposition Author(s): Andrei, S.A., Thijssen, V., Brunsveld, L., Ottmann, C., Milroy, L.G.

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Funding Organization	Location	Grant Number
Netherlands Organisation for Scientific Research	Netherlands	ECHO-STIP 717.014.001
Netherlands Organisation for Scientific Research	Netherlands	Gravity program 024.001.035

Revision History  

• Version 1.0: 2019-04-17
  Type: Initial release
  
• Version 1.1: 2019-12-04
  Changes: Database references
• Version 1.2: 2019-12-18
  Changes: Database references
• Version 2.0: 2022-12-07
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
• Version 3.0: 2023-11-15
  Changes: Atomic model, Data collection
• Version 3.1: 2024-01-31
  Changes: Refinement description