8DGM | pdb_00008dgm

14-3-3 epsilon bound to phosphorylated PEAK1 (pT1165) peptide

• PDB DOI: https://doi.org/10.2210/pdb8DGM/pdb

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


• Deposited: 2022-06-24 Released: 2023-06-07 
• Deposition Author(s): Roy, M.J., Hardy, J.M., Lucet, I.S.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.266 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

Structural mapping of PEAK pseudokinase interactions identifies 14-3-3 as a molecular switch for PEAK3 signaling.

Roy, M.J., Surudoi, M.G., Kropp, A., Hou, J., Dai, W., Hardy, J.M., Liang, L.Y., Cotton, T.R., Lechtenberg, B.C., Dite, T.A., Ma, X., Daly, R.J., Patel, O., Lucet, I.S.

(2023) Nat Commun 14: 3542-3542

• PubMed: 37336884 
• DOI: https://doi.org/10.1038/s41467-023-38869-9
• Primary Citation Related Structures: 
  8DGM, 8DGN, 8DGO, 8DGP


• PubMed Abstract: 
  

  PEAK pseudokinases regulate cell migration, invasion and proliferation by recruiting key signaling proteins to the cytoskeleton. Despite lacking catalytic activity, alteration in their expression level is associated with several aggressive cancers. Here, we elucidate the molecular details of key PEAK signaling interactions with the adapter proteins CrkII and Grb2 and the scaffold protein 14-3-3. Our findings rationalize why the dimerization of PEAK proteins has a crucial function in signal transduction and provide biophysical and structural data to unravel binding specificity within the PEAK interactome. We identify a conserved high affinity 14-3-3 motif on PEAK3 and demonstrate its role as a molecular switch to regulate CrkII binding and signaling via Grb2. Together, our studies provide a detailed structural snapshot of PEAK interaction networks and further elucidate how PEAK proteins, especially PEAK3, act as dynamic scaffolds that exploit adapter proteins to control signal transduction in cell growth/motility and cancer.

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Organizational Affiliation: 
• The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia. [e-mail].
Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia. [e-mail].
The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.
Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia.
Cancer Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia.
Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia.
The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia. [e-mail].
Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: surface plasmon resonance

Macromolecule Content 

• Total Structure Weight: 31.91 kDa 
• Atom Count: 1,499 
• Modeled Residue Count: 206 
• Deposited Residue Count: 278 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
14-3-3 protein epsilon	A	258	Homo sapiens	Mutation(s): 0  Gene Names: YWHAE
UniProt & NIH Common Fund Data Resources
Find proteins for P62258 (Homo sapiens) Explore P62258  Go to UniProtKB:  P62258
PHAROS:  P62258 GTEx:  ENSG00000108953

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Inactive tyrosine-protein kinase PEAK1	B	20	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H792 (Homo sapiens) Explore Q9H792  Go to UniProtKB:  Q9H792
PHAROS:  Q9H792 GTEx:  ENSG00000173517

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	B	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.266 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.423	α = 90
b = 91.423	β = 90
c = 139.872	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-06-07 
Deposition Author(s): Roy, M.J., Hardy, J.M., Lucet, I.S.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	APP1144149

Revision History  

• Version 1.0: 2023-06-07
  Type: Initial release
  
• Version 1.1: 2023-07-12
  Changes: Data collection, Database references
• Version 1.2: 2023-08-16
  Changes: Data collection
• Version 1.3: 2023-10-25
  Changes: Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary