6JF0 | pdb_00006jf0

Covalent labeling of hPPARg-LBD by turn-on fluorescent probe mediated by conjugate addition and cyclization

• PDB DOI: https://doi.org/10.2210/pdb6JF0/pdb

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


• Deposited: 2019-02-07 Released: 2020-02-12 
• Deposition Author(s): Kojima, H., Yamamoto, K., Itoh, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 
  0.296 (Depositor), 0.287 (DCC) 
• R-Value Work: 
  0.267 (Depositor), 0.263 (DCC) 
• R-Value Observed: 
  0.268 (Depositor) 

Starting Model: experimental

Literature

Cyclization Reaction-Based Turn-on Probe for Covalent Labeling of Target Proteins.

Kojima, H., Fujita, Y., Takeuchi, R., Ikebe, Y., Ohashi, N., Yamamoto, K., Itoh, T.

(2020) Cell Chem Biol 27: 334

• PubMed: 31991094 
• DOI: https://doi.org/10.1016/j.chembiol.2020.01.006
• Primary Citation Related Structures: 
  6JEY, 6JEZ, 6JF0


• PubMed Abstract: 
  

  Fluorescent molecules have contributed to basic biological research but there are currently only a limited number of probes available for the detection of non-enzymatic proteins. Here, we report turn-on fluorescent probes mediated by conjugate addition and cyclization (TCC probes). These probes react with multiple amino acids and exhibit a 36-fold greater emission intensity after reaction. We analyzed the reactions between TCC probes and nuclear receptors by electrospray ionization mass spectrometry, X-ray crystallography, spectrofluorometry, and fluorescence microscopy. In vitro analysis showed that probes consisting of a protein ligand and TCC could label vitamin D receptor and peroxisome proliferator-activated receptor γ. Moreover, we demonstrated that not only a ligand unit but also a peptide unit can label the target protein in a complex mixture.

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Organizational Affiliation: 
• Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan.
Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 63.62 kDa 
• Atom Count: 4,053 
• Modeled Residue Count: 503 
• Deposited Residue Count: 552 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor gamma	A, B	276	Homo sapiens	Mutation(s): 0  Gene Names: PPARG, NR1C3
UniProt & NIH Common Fund Data Resources
Find proteins for P37231 (Homo sapiens) Explore P37231  Go to UniProtKB:  P37231
PHAROS:  P37231 GTEx:  ENSG00000132170

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EB6	C [auth A]	methyl (2~{S})-3-[4-[3-(4-methoxy-2-oxidanyl-phenyl)prop-2-ynoyloxy]phenyl]-2-[[2-(phenylcarbonyl)phenyl]amino]propanoate C33 H27 N O7 CEHNFAIQCQNZKE-LJAQVGFWSA-N
EBF	D [auth B]	7-methoxychromen-2-one C10 H8 O3 LIIALPBMIOVAHH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free:  0.296 (Depositor), 0.287 (DCC) 
• R-Value Work:  0.267 (Depositor), 0.263 (DCC) 
• R-Value Observed: 0.268 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.12	α = 90
b = 61.23	β = 102.26
c = 117.37	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-02-12 
Deposition Author(s): Kojima, H., Yamamoto, K., Itoh, T.

Revision History  

• Version 1.0: 2020-02-12
  Type: Initial release
  
• Version 1.1: 2020-04-08
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description