3CFC | pdb_00003cfc

High-resolution structure of blue fluorescent antibody EP2-19G2

• PDB DOI: https://doi.org/10.2210/pdb3CFC/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Mutation(s): No 


• Deposited: 2008-03-03 Released: 2008-03-18 
• Deposition Author(s): Debler, E.W., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.231 (Depositor), 0.294 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.261 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Deeply inverted electron-hole recombination in a luminescent antibody-stilbene complex.

Debler, E.W., Kaufmann, G.F., Meijler, M.M., Heine, A., Mee, J.M., Pljevaljcic, G., Di Bilio, A.J., Schultz, P.G., Millar, D.P., Janda, K.D., Wilson, I.A., Gray, H.B., Lerner, R.A.

(2008) Science 319: 1232-1235

• PubMed: 18309081 
• DOI: https://doi.org/10.1126/science.1153445
• Primary Citation Related Structures: 
  3CFB, 3CFC, 3CFD, 3CFE


• PubMed Abstract: 
  

  The blue-emissive antibody EP2-19G2 that has been elicited against trans-stilbene has unprecedented ability to produce bright luminescence and has been used as a biosensor in various applications. We show that the prolonged luminescence is not stilbene fluorescence. Instead, the emissive species is a charge-transfer excited complex of an anionic stilbene and a cationic, parallel pi-stacked tryptophan. Upon charge recombination, this complex generates exceptionally bright blue light. Complex formation is enabled by a deeply penetrating ligand-binding pocket, which in turn results from a noncanonical interface between the two variable domains of the antibody.

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Organizational Affiliation: 
• Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 46.92 kDa 
• Atom Count: 3,703 
• Modeled Residue Count: 432 
• Deposited Residue Count: 432 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BLUE FLUORESCENT ANTIBODY EP2-19G2-IGG2B HEAVY CHAIN	A [auth H]	213	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BLUE FLUORESCENT ANTIBODY EP2-19G2-KAPPA LIGHT CHAIN	B [auth L]	219	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P01837 (Mus musculus) Explore P01837  Go to UniProtKB:  P01837
Find proteins for P03976 (Mus musculus) Explore P03976  Go to UniProtKB:  P03976
UniProt Groups	P03976P01837

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth H]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.231 (Depositor), 0.294 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.261 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.891	α = 90
b = 87.891	β = 90
c = 114.111	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-18 
Deposition Author(s): Debler, E.W., Wilson, I.A.

Revision History  

• Version 1.0: 2008-03-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary