6WZN | pdb_00006wzn

Crystal Structure of a Fluorescent Single Chain Fv Chimera

• PDB DOI: https://doi.org/10.2210/pdb6WZN/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-05-14 Released: 2021-01-27 
• Deposition Author(s): Close, D., Velappan, N., Hung, L.W., Naranjo, L., Hemez, C., DeVore, N., McCullough, D., Lillo, A.M., Waldo, G., Bradbury, A.R.M.
• Funding Organization(s): Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.211 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

Construction, characterization and crystal structure of a fluorescent single-chain Fv chimera.

Velappan, N., Close, D., Hung, L.W., Naranjo, L., Hemez, C., DeVore, N., McCullough, D.K., Lillo, A.M., Waldo, G.S., Bradbury, A.R.M.

(2021) Protein Eng Des Sel 34

• PubMed: 33586761 
• DOI: https://doi.org/10.1093/protein/gzaa029
• Primary Citation Related Structures: 
  6WZN


• PubMed Abstract: 
  

  In vitro display technologies based on phage and yeast have a successful history of selecting single-chain variable fragment (scFv) antibodies against various targets. However, single-chain antibodies are often unstable and poorly expressed in Escherichia coli. Here, we explore the feasibility of converting scFv antibodies to an intrinsically fluorescent format by inserting the monomeric, stable fluorescent protein named thermal green, between the light- and heavy-chain variable regions. Our results show that the scTGP format maintains the affinity and specificity of the antibodies, improves expression levels, allows one-step fluorescent assay for detection of binding and is a suitable reagent for epitope binning. We also report the crystal structure of an scTGP construct that recognizes phosphorylated tyrosine on FcεR1 receptor of the allergy pathway.

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Organizational Affiliation: 
• Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
Microbiology Department, University of Tennessee, Knoxville, TN 37996, USA.
ARUP Laboratories, Institute for Clinical and Experimental Pathology, Salt Lake City, UT 84108, USA.
Specifica Inc., Santa Fe, NM 87505, USA.
Graduate Program in Biophysics, Harvard University, Boston, MA 02115 USA.
Chemistry Department, Missouri State University, Springfield, MO 65897, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 51.08 kDa 
• Atom Count: 3,706 
• Modeled Residue Count: 460 
• Deposited Residue Count: 463 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fluorescent Single Chain Fv Chimera	A	463	synthetic construct	Mutation(s): 0

Small Molecules

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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CRQ	A	L-PEPTIDE LINKING	C16 H16 N4 O5		GLN, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.211 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.961	α = 90
b = 103.961	β = 90
c = 122.74	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-01-27 
Deposition Author(s): Close, D., Velappan, N., Hung, L.W., Naranjo, L., Hemez, C., DeVore, N., McCullough, D., Lillo, A.M., Waldo, G., Bradbury, A.R.M.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	P50GM085273

Revision History  

• Version 1.0: 2021-01-27
  Type: Initial release
  
• Version 1.1: 2021-02-10
  Changes: Source and taxonomy
• Version 1.2: 2021-03-03
  Changes: Database references
• Version 1.3: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2024-10-30
  Changes: Structure summary
• Version 3.0: 2026-03-18
  Changes: Polymer sequence