3GL4

X-ray structure of photobleached killerred


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.232 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structural basis for phototoxicity of the genetically encoded photosensitizer KillerRed.

Pletnev, S.Gurskaya, N.G.Pletneva, N.V.Lukyanov, K.A.Chudakov, D.M.Martynov, V.I.Popov, V.O.Kovalchuk, M.V.Wlodawer, A.Dauter, Z.Pletnev, V.

(2009) J Biol Chem 284: 32028-32039

  • DOI: https://doi.org/10.1074/jbc.M109.054973
  • Primary Citation of Related Structures:  
    3GB3, 3GL4

  • PubMed Abstract: 

    KillerRed is the only known fluorescent protein that demonstrates notable phototoxicity, exceeding that of the other green and red fluorescent proteins by at least 1,000-fold. KillerRed could serve as an instrument to inactivate target proteins or to kill cell populations in photodynamic therapy. However, the nature of KillerRed phototoxicity has remained unclear, impeding the development of more phototoxic variants. Here we present the results of a high resolution crystallographic study of KillerRed in the active fluorescent and in the photobleached non-fluorescent states. A unique and striking feature of the structure is a water-filled channel reaching the chromophore area from the end cap of the beta-barrel that is probably one of the key structural features responsible for phototoxicity. A study of the structure-function relationship of KillerRed, supported by structure-based, site-directed mutagenesis, has also revealed the key residues most likely responsible for the phototoxic effect. In particular, Glu(68) and Ser(119), located adjacent to the chromophore, have been assigned as the primary trigger of the reaction chain.


  • Organizational Affiliation

    Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute/SAIC-Frederick Inc., Frederick, Maryland 21702, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
KillerRed
A, B
235Anthomedusae sp. DC-2005Mutation(s): 1 
UniProt
Find proteins for Q2TCH5 (Anthomedusae sp. DC-2005)
Explore Q2TCH5 
Go to UniProtKB:  Q2TCH5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2TCH5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CRQ
Query on CRQ
A, B
L-PEPTIDE LINKINGC16 H16 N4 O5GLN, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.232 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.218α = 90
b = 73.781β = 90
c = 76.178γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations