3T0X

Fluorogen Activating Protein M8VLA4(S55P) in complex with dimethylindole red

Summary for 3T0X

• Entry DOI: 10.2210/pdb3t0x/pdb
• Related: 3T0V 3T0W
• Descriptor: Immunoglobulin variable lambda domain M8VLA4(S55P), 1-(3-sulfopropyl)-4-[(1E,3E)-3-(1,3,3-trimethyl-1,3-dihydro-2H-indol-2-ylidene)prop-1-en-1-yl]quinolinium, 1,2-ETHANEDIOL, ... (5 entities in total)
• Functional Keywords: immunoglobulin fold, fluorogen activation, dimethylindole red, dye-binding protein
• Biological source: Homo sapiens
• Total number of polymer chains: 2
• Total formula weight: 27408.63

Authors

Stanfield, R.,Senutovitch, N.,Bhattacharyya, S.,Rule, G.,Wilson, I.A.,Armitage, B.,Waggoner, A.S.,Berget, P. (deposition date: 2011-07-20, release date: 2012-03-21, Last modification date: 2024-11-20)

Primary citation

Senutovitch, N.,Stanfield, R.L.,Bhattacharyya, S.,Rule, G.S.,Wilson, I.A.,Armitage, B.A.,Waggoner, A.S.,Berget, P.B.
A variable light domain fluorogen activating protein homodimerizes to activate dimethylindole red.
Biochemistry, 51:2471-2485, 2012

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.

PubMed: 22390683
DOI: 10.1021/bi201422g

Experimental method

X-RAY DIFFRACTION (1.96 Å)