4I3B

Crystal structure of fluorescent protein UnaG wild type


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.199 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.129 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A bilirubin-inducible fluorescent protein from eel muscle

Kumagai, A.Ando, R.Miyatake, H.Greimel, P.Kobayashi, T.Hirabayashi, Y.Shimogori, T.Miyawaki, A.

(2013) Cell 153: 1602-1611

  • DOI: 10.1016/j.cell.2013.05.038
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The fluorescent protein toolbox has revolutionized experimental biology. Despite this advance, no fluorescent proteins have been identified from vertebrates, nor has chromogenic ligand-inducible activation or clinical utility been demonstrated. Here, ...

    The fluorescent protein toolbox has revolutionized experimental biology. Despite this advance, no fluorescent proteins have been identified from vertebrates, nor has chromogenic ligand-inducible activation or clinical utility been demonstrated. Here, we report the cloning and characterization of UnaG, a fluorescent protein from Japanese eel. UnaG belongs to the fatty-acid-binding protein (FABP) family, and expression in eel is restricted to small-diameter muscle fibers. On heterologous expression in cell lines or mouse brain, UnaG produces oxygen-independent green fluorescence. Remarkably, UnaG fluorescence is triggered by an endogenous ligand, bilirubin, a membrane-permeable heme metabolite and clinical health biomarker. The holoUnaG structure at 1.2 Å revealed a biplanar coordination of bilirubin by reversible π-conjugation, and we used this high-affinity and high-specificity interaction to establish a fluorescence-based human bilirubin assay with promising clinical utility. UnaG will be the prototype for a versatile class of ligand-activated fluorescent proteins, with applications in research, medicine, and bioengineering.


    Organizational Affiliation

    Cell Function Dynamics, Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako-city, Saitama 351-0198, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bilirubin-inducible fluorescent protein UnaG
A, B, C, D, E, F
139Anguilla japonicaMutation(s): 0 
Find proteins for P0DM59 (Anguilla japonica)
Go to UniProtKB:  P0DM59
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BLR
Query on BLR

Download SDF File 
Download CCD File 
A, B, C, D, E, F
3-[5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-2-[[5-[(Z)-(3-ethenyl-4-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1H-pyrrol-2-yl]methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid
Bilirubin IX alpha
C33 H36 N4 O6
BPYKTIZUTYGOLE-IFADSCNNSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A, B, D, E, F
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.199 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.129 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 44.394α = 90.00
b = 73.954β = 92.45
c = 124.364γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXphasing
HKL-2000data collection
HKL-2000data scaling
PHENIXmodel building
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-06-19
    Type: Initial release
  • Version 1.1: 2013-07-31
    Type: Database references
  • Version 1.2: 2015-02-04
    Type: Database references, Non-polymer description