7A6Y | pdb_00007a6y

Structure of 14-3-3 gamma in complex with DAPK2 peptide stabilized by FC-A

• PDB DOI: https://doi.org/10.2210/pdb7A6Y/pdb

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


• Deposited: 2020-08-27 Released: 2021-08-25 
• Deposition Author(s): Horvath, M., Obsilova, V., Obsil, T.
• Funding Organization(s): Grant Agency of the Czech Republic

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.259 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

14-3-3 proteins inactivate DAPK2 by promoting its dimerization and protecting key regulatory phosphosites.

Horvath, M., Petrvalska, O., Herman, P., Obsilova, V., Obsil, T.

(2021) Commun Biol 4: 986-986

• PubMed: 34413451 
• DOI: https://doi.org/10.1038/s42003-021-02518-y
• Primary Citation Related Structures: 
  7A6R, 7A6Y


• PubMed Abstract: 
  

  Death-associated protein kinase 2 (DAPK2) is a CaM-regulated Ser/Thr protein kinase, involved in apoptosis, autophagy, granulocyte differentiation and motility regulation, whose activity is controlled by autoinhibition, autophosphorylation, dimerization and interaction with scaffolding proteins 14-3-3. However, the structural basis of 14-3-3-mediated DAPK2 regulation remains unclear. Here, we structurally and biochemically characterize the full-length human DAPK2:14-3-3 complex by combining several biophysical techniques. The results from our X-ray crystallographic analysis revealed that Thr369 phosphorylation at the DAPK2 C terminus creates a high-affinity canonical mode III 14-3-3-binding motif, further enhanced by the diterpene glycoside Fusicoccin A. Moreover, concentration-dependent DAPK2 dimerization is disrupted by Ca ²⁺ /CaM binding and stabilized by 14-3-3 binding in solution, thereby protecting the DAPK2 inhibitory autophosphorylation site Ser318 against dephosphorylation and preventing Ca ²⁺ /CaM binding. Overall, our findings provide mechanistic insights into 14-3-3-mediated DAPK2 inhibition and highlight the potential of the DAPK2:14-3-3 complex as a target for anti-inflammatory therapies.

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Organizational Affiliation: 
• Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Prague, Czech Republic.
Department of Structural Biology of Signaling Proteins, Division BIOCEV, Institute of Physiology of the Czech Academy of Sciences, Vestec, Czech Republic.
Institute of Physics, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic.
Department of Structural Biology of Signaling Proteins, Division BIOCEV, Institute of Physiology of the Czech Academy of Sciences, Vestec, Czech Republic. [e-mail].
Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Prague, Czech Republic. [e-mail].
Department of Structural Biology of Signaling Proteins, Division BIOCEV, Institute of Physiology of the Czech Academy of Sciences, Vestec, Czech Republic. [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: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 114.57 kDa 
• Atom Count: 7,579 
• Modeled Residue Count: 921 
• Deposited Residue Count: 972 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
14-3-3 protein gamma	A, B, C, D	236	Homo sapiens	Mutation(s): 0  Gene Names: YWHAG
UniProt & NIH Common Fund Data Resources
Find proteins for P61981 (Homo sapiens) Explore P61981  Go to UniProtKB:  P61981
PHAROS:  P61981 GTEx:  ENSG00000170027

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DAPK2 C-terminal peptide	E [auth J], F [auth K], G [auth L], H [auth M]	7	Homo sapiens	Mutation(s): 0  EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UIK4 (Homo sapiens) Explore Q9UIK4  Go to UniProtKB:  Q9UIK4
PHAROS:  Q9UIK4 GTEx:  ENSG00000035664

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FSC	I [auth A], J [auth C], K [auth D]	FUSICOCCIN C36 H56 O12 KXTYBXCEQOANSX-WYKQKOHHSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	E [auth J], F [auth K], G [auth L], H [auth M]	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.259 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 205.502	α = 90
b = 205.502	β = 90
c = 74.274	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-08-25 
Deposition Author(s): Horvath, M., Obsilova, V., Obsil, T.

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Funding Organization	Location	Grant Number
Grant Agency of the Czech Republic	Czech Republic	19-00121S

Revision History  

• Version 1.0: 2021-08-25
  Type: Initial release
  
• Version 1.1: 2021-09-22
  Changes: Data collection, Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary