4XTQ

Crystal structure of a mutant (C20S) of a near-infrared fluorescent protein BphP1-FP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular Basis of Spectral Diversity in Near-Infrared Phytochrome-Based Fluorescent Proteins.

Shcherbakova, D.M.Baloban, M.Pletnev, S.Malashkevich, V.N.Xiao, H.Dauter, Z.Verkhusha, V.V.

(2015) Chem.Biol. 22: 1540-1551

  • DOI: 10.1016/j.chembiol.2015.10.007

  • PubMed Abstract: 
  • Near-infrared fluorescent proteins (NIR FPs) engineered from bacterial phytochromes (BphPs) are the probes of choice for deep-tissue imaging. Detection of several processes requires spectrally distinct NIR FPs. We developed an NIR FP, BphP1-FP, which ...

    Near-infrared fluorescent proteins (NIR FPs) engineered from bacterial phytochromes (BphPs) are the probes of choice for deep-tissue imaging. Detection of several processes requires spectrally distinct NIR FPs. We developed an NIR FP, BphP1-FP, which has the most blue-shifted spectra and the highest fluorescence quantum yield among BphP-derived FPs. We found that these properties result from the binding of the biliverdin chromophore to a cysteine residue in the GAF domain, unlike natural BphPs and other BphP-based FPs. To elucidate the molecular basis of the spectral shift, we applied biochemical, structural and mass spectrometry analyses and revealed the formation of unique chromophore species. Mutagenesis of NIR FPs of different origins indicated that the mechanism of the spectral shift is general and can be used to design multicolor NIR FPs from other BphPs. We applied pairs of spectrally distinct point cysteine mutants to multicolor cell labeling and demonstrated that they perform well in model deep-tissue imaging.


    Organizational Affiliation

    Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BphP1-FP/C20S
A
327Rhodopseudomonas palustris (strain TIE-1)Mutation(s): 0 
Find proteins for B3Q7C0 (Rhodopseudomonas palustris (strain TIE-1))
Go to UniProtKB:  B3Q7C0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BL8
Query on BL8

Download SDF File 
Download CCD File 
A
3-[2-[(Z)-[5-[(Z)-[(3R,4R)-3-ethenyl-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-pyrrol-2-ylidene]methyl]-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid
C33 H36 N4 O6
WLDQKQLRZDEERT-IFTFHFPBSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.656α = 90.00
b = 53.113β = 90.00
c = 107.070γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
REFMACrefinement
SCALEPACKdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer InstituteUnited StatesCA164468
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM073913
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM108579
EU FP7 ProgramFinlandERC-2013-ADG-340233
National Institutes of Health/National Cancer InstituteUnited StatesHHSN261200800001E

Revision History 

  • Version 1.0: 2015-12-09
    Type: Initial release
  • Version 1.1: 2015-12-16
    Type: Database references
  • Version 1.2: 2017-09-06
    Type: Author supporting evidence, Database references, Derived calculations