7AV6

FAST in a domain-swapped dimer form

• PDB DOI: https://doi.org/10.2210/pdb7AV6/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Halorhodospira halophila
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-11-04 Released: 2021-06-09 
• Deposition Author(s): Bukhdruker, S., Remeeva, A., Ruchkin, D., Gorbachev, D., Povarova, N., Mineev, K., Goncharuk, S., Baranov, M., Mishin, A., Borshchevskiy, V.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.237 
• R-Value Work: 0.214 
• R-Value Observed: 0.215 

Literature

NanoFAST: structure-based design of a small fluorogen-activating protein with only 98 amino acids.

Mineev, K.S., Goncharuk, S.A., Goncharuk, M.V., Povarova, N.V., Sokolov, A.I., Baleeva, N.S., Smirnov, A.Y., Myasnyanko, I.N., Ruchkin, D.A., Bukhdruker, S., Remeeva, A., Mishin, A., Borshchevskiy, V., Gordeliy, V., Arseniev, A.S., Gorbachev, D.A., Gavrikov, A.S., Mishin, A.S., Baranov, M.S.

(2021) Chem Sci 12: 6719-6725

• PubMed: 34040747 
• DOI: https://doi.org/10.1039/d1sc01454d
• Primary Citation of Related Structures:  
  7AV6, 7AVA, 7AVB


• PubMed Abstract: 
  

  One of the essential characteristics of any tag used in bioscience and medical applications is its size. The larger the label, the more it may affect the studied object, and the more it may distort its behavior. In this paper, using NMR spectroscopy and X-ray crystallography, we have studied the structure of fluorogen-activating protein FAST both in the apo form and in complex with the fluorogen. We showed that significant change in the protein occurs upon interaction with the ligand. While the protein is completely ordered in the complex, its apo form is characterized by higher mobility and disordering of its N-terminus. We used structural information to design the shortened FAST (which we named nanoFAST) by truncating 26 N-terminal residues. Thus, we created the shortest genetically encoded tag among all known fluorescent and fluorogen-activating proteins, which is composed of only 98 amino acids.

---

Organizational Affiliation: 

Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 15.34 kDa 
• Atom Count: 793 
• Modelled Residue Count: 99 
• Deposited Residue Count: 138 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photoactive yellow protein	A	138	Halorhodospira halophila	Mutation(s): 9  Gene Names: pyp
UniProt
Find proteins for P16113 (Halorhodospira halophila) Explore P16113  Go to UniProtKB:  P16113

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMT	B [auth A], C [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.237 
• R-Value Work: 0.214 
• R-Value Observed: 0.215 
• Space Group: P 4₁ 2₁ 2
• Diffraction Data: https://doi.org/10.18430/m37av6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.92	α = 90
b = 45.92	β = 90
c = 105.04	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
XDS	data reduction
XSCALE	data scaling
MoRDa	phasing
ARP/wARP	model building
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-06-09 
Deposition Author(s): Bukhdruker, S., Remeeva, A., Ruchkin, D., Gorbachev, D., Povarova, N., Mineev, K., Goncharuk, S., Baranov, M., Mishin, A., Borshchevskiy, V.

Revision History  

• Version 1.0: 2021-06-09
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Database references, Refinement description