5ZAU | pdb_00005zau

Complex of the human FYN SH3 and monobody binder

• PDB DOI: https://doi.org/10.2210/pdb5ZAU/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens, Saccharolobus solfataricus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-02-09 Released: 2019-09-11 
• Deposition Author(s): Reddy, P.P., Gulyani, A., Das, R.
• Funding Organization(s): TIFR

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

A Fyn biosensor reveals pulsatile, spatially localized kinase activity and signaling crosstalk in live mammalian cells.

Mukherjee, A., Singh, R., Udayan, S., Biswas, S., Reddy, P.P., Manmadhan, S., George, G., Kumar, S., Das, R., Rao, B.M., Gulyani, A.

(2020) Elife 9

• PubMed: 32017701 
• DOI: https://doi.org/10.7554/eLife.50571
• Primary Citation Related Structures: 
  5ZAU


• PubMed Abstract: 
  

  Cell behavior is controlled through spatio-temporally localized protein activity. Despite unique and often contradictory roles played by Src-family-kinases (SFKs) in regulating cell physiology, activity patterns of individual SFKs have remained elusive. Here, we report a biosensor for specifically visualizing active conformation of SFK-Fyn in live cells. We deployed combinatorial library screening to isolate a binding-protein (F29) targeting activated Fyn. Nuclear-magnetic-resonance (NMR) analysis provides the structural basis of F29 specificity for Fyn over homologous SFKs. Using F29, we engineered a sensitive, minimally-perturbing fluorescence-resonance-energy-transfer (FRET) biosensor ( FynSensor ) that reveals cellular Fyn activity to be spatially localized, pulsatile and sensitive to adhesion/integrin signaling. Strikingly, growth factor stimulation further enhanced Fyn activity in pre-activated intracellular zones. However, inhibition of focal-adhesion-kinase activity not only attenuates Fyn activity, but abolishes growth-factor modulation. FynSensor imaging uncovers spatially organized, sensitized signaling clusters, direct crosstalk between integrin and growth-factor-signaling, and clarifies how compartmentalized Src-kinase activity may drive cell fate.

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Organizational Affiliation: 
• Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India.
SASTRA University, Thanjavur, India.
National Centre for Biological Sciences, Bangalore, India.
North Carolina State University, Raleigh, United States.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 13.89 kDa 
• Atom Count: 983 
• Modeled Residue Count: 121 
• Deposited Residue Count: 121 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase Fyn	A	57	Homo sapiens	Mutation(s): 0  Gene Names: FYN EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P06241 (Homo sapiens) Explore P06241  Go to UniProtKB:  P06241
PHAROS:  P06241 GTEx:  ENSG00000010810

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Monobody Binder	B	64	Saccharolobus solfataricus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-09-11 
Deposition Author(s): Reddy, P.P., Gulyani, A., Das, R.

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Funding Organization	Location	Grant Number
TIFR	India	--

Revision History  

• Version 1.0: 2019-09-11
  Type: Initial release
  
• Version 1.1: 2020-03-25
  Changes: Database references
• Version 1.2: 2023-06-14
  Changes: Database references, Other
• Version 1.3: 2024-05-15
  Changes: Data collection, Database references