6UBO

Fluorogen Activating Protein Dib1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure-Based Rational Design of Two Enhanced Bacterial Lipocalin Blc Tags for Protein-PAINT Super-resolution Microscopy.

Muslinkina, L.Gavrikov, A.S.Bozhanova, N.G.Mishin, A.S.Baranov, M.S.Meiler, J.Pletneva, N.V.Pletnev, V.Z.Pletnev, S.

(2020) ACS Chem Biol 15: 2456-2465

  • DOI: https://doi.org/10.1021/acschembio.0c00440
  • Primary Citation of Related Structures:  
    6UBO

  • PubMed Abstract: 

    Super-resolution fluorescent imaging in living cells remains technically challenging, largely due to the photodecomposition of fluorescent tags. The recently suggested protein-PAINT is the only super-resolution technique available for prolonged imaging of proteins in living cells. It is realized with complexes of fluorogen-activating proteins, expressed as fusions, and solvatochromic synthetic dyes. Once photobleached, the dye in the complex is replaced with a fresh fluorogen available in the sample. With suitable kinetics, this replacement creates fluorescence blinking required for attaining super-resolution and overcomes photobleaching associated with the loss of an irreplaceable fluorophore. Here we report on the rational design of two protein-PAINT tags based on the 1.58 Å crystal structure of the DiB1:M739 complex, an improved green-emitting DiB3/F74V:M739 and a new orange-emitting DiB3/F53L:M739. They outperform previously reported DiB-based tags to become best in class biomarkers for protein-PAINT. The new tags advance protein-PAINT from the proof-of-concept to a reliable tool suitable for prolonged super-resolution imaging of intracellular proteins in fixed and living cells and two-color PAINT-like nanoscopy with a single fluorogen.


  • Organizational Affiliation

    Basic Research Program, Frederick National Laboratory for Cancer Research, Argonne, Illinois 60439, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Outer membrane lipoprotein Blc
A, B
177Escherichia coli K-12Mutation(s): 0 
Gene Names: blcyjeLb4149JW4110
UniProt
Find proteins for P0A901 (Escherichia coli (strain K12))
Explore P0A901 
Go to UniProtKB:  P0A901
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A901
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P4K
Query on P4K

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
polyethylene glycol
C30 H62 O15
WWPGFZAAWXFBTF-UHFFFAOYSA-N
Q3J (Subject of Investigation/LOI)
Query on Q3J

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
12-(diethylamino)-2,2-bis(fluoranyl)-4,5-dimethyl-5-aza-3-azonia-2-boranuidatricyclo[7.4.0.0^{3,7}]trideca-1(13),3,7,9,11-pentaen-6-one
C16 H20 B F2 N3 O
OOEJBECJAKZKRT-UHFFFAOYSA-N
CIT
Query on CIT

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.843α = 90
b = 44.843β = 90
c = 158.235γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
SERGUIdata collection
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-16
    Type: Initial release
  • Version 1.1: 2021-03-31
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description