3CFD

Purple-fluorescent antibody EP2-25C10 in complex with its stilbene hapten

• PDB DOI: https://doi.org/10.2210/pdb3CFD/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., Heine, A., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.243 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.212 (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 of 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)

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 95.53 kDa 
• Atom Count: 6,824 
• Modelled Residue Count: 865 
• Deposited Residue Count: 868 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PURPLE-FLUORESCENT ANTIBODY EP2-25C10-KAPPA LIGHT CHAIN	A [auth L], C [auth A]	214	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PURPLE-FLUORESCENT ANTIBODY EP2-25C10-IGG2B HEAVY CHAIN	B [auth H], D [auth B]	220	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SPB	E [auth H], G [auth B]	4-(4-STYRYL-PHENYLCARBAMOYL)-BUTYRIC ACID C19 H19 N O3 FTXJWRRYLLRFMG-MDZDMXLPSA-N
GOL	F [auth H]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.243 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.99	α = 91.98
b = 72.48	β = 106.11
c = 77.23	γ = 114.15

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., Heine, A., Wilson, I.A.

Revision History  

• Version 1.0: 2008-03-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-09
  Changes: Structure summary