Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 14.48 kDa 
• Atom Count: 1052 
• Modelled Residue Count: 113 
• Deposited Residue Count: 123 
• Unique protein chains: 1

3T0V

Unliganded fluorogen activating protein M8VL

• PDB DOI: 10.2210/pdb3T0V/pdb

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


• Deposited: 2011-07-20 Released: 2012-03-21 
• Deposition Author(s): Stanfield, R., Senutovitch, N., Bhattacharyya, S., Rule, G., Wilson, I.A., Armitage, B., Waggoner, A.S., Berget, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.208 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 

Literature

A variable light domain fluorogen activating protein homodimerizes to activate dimethylindole red.

Senutovitch, N., Stanfield, R.L., Bhattacharyya, S., Rule, G.S., Wilson, I.A., Armitage, B.A., Waggoner, A.S., Berget, P.B.

(2012) Biochemistry 51: 2471-2485

• PubMed: 22390683 
• DOI: 10.1021/bi201422g
• Primary Citation of Related Structures:  
  3T0V, 3T0W, 3T0X


• PubMed Abstract: 
  

Novel fluorescent tools such as green fluorescent protein analogues and fluorogen activating proteins (FAPs) are useful in biological imaging for tracking protein dynamics in real time with a low fluorescence background. FAPs are single-chain variable fragments (scFvs) selected from a yeast surface display library that produce fluorescence upon binding a specific dye or fluorogen that is normally not fluorescent when present in solution. FAPs generally consist of human immunoglobulin variable heavy (V(H)) and variable light (V(L)) domains covalently attached via a glycine- and serine-rich linker. Previously, we determined that the yeast surface clone, V(H)-V(L) M8, could bind and activate the fluorogen dimethylindole red (DIR) but that the fluorogen activation properties were localized to the M8V(L) domain. We report here that both nuclear magnetic resonance and X-ray diffraction methods indicate the M8V(L) forms noncovalent, antiparallel homodimers that are the fluorogen activating species. The M8V(L) homodimers activate DIR by restriction of internal rotation of the bound dye. These structural results, together with directed evolution experiments with both V(H)-V(L) M8 and M8V(L), led us to rationally design tandem, covalent homodimers of M8V(L) domains joined by a flexible linker that have a high affinity for DIR and good quantum yields.

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Organizational Affiliation: 

The Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
immunoglobulin variable lambda domain	A	123	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PE3	C [auth A]	3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL C28 H58 O15 ILLKMACMBHTSHP-UHFFFAOYSA-N
1PE	B [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
TRS	H [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
SO4	G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.208 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.663	α = 90
b = 93.639	β = 90
c = 30.573	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-07-20 
• Released Date: 2012-03-21 
Deposition Author(s): Stanfield, R., Senutovitch, N., Bhattacharyya, S., Rule, G., Wilson, I.A., Armitage, B., Waggoner, A.S., Berget, P.

Revision History  

• Version 1.0: 2012-03-21
  Type: Initial release
  
• Version 1.1: 2012-03-28
  Changes: Other
• Version 1.2: 2012-04-11
  Changes: Database references
• Version 2.0: 2019-12-25
  Changes: Advisory, Derived calculations, Polymer sequence