6LOF | pdb_00006lof

Crystal structure of ZsYellow soaked by Cu2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.215 (Depositor), 0.215 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Literature

Spectroscopic and Structural Analysis of Cu 2+ -Induced Fluorescence Quenching of ZsYellow.

Kim, I.J.Xu, Y.Nam, K.H.

(2020) Biosensors (Basel) 10

  • DOI: https://doi.org/10.3390/bios10030029
  • Primary Citation Related Structures: 
    6LOF

  • PubMed Abstract: 

    Fluorescent proteins exhibit fluorescence quenching by specific transition metals, suggesting their potential as fluorescent protein-based metal biosensors. Each fluorescent protein exhibits unique spectroscopic properties and mechanisms for fluorescence quenching by metals. Therefore, the metal-induced fluorescence quenching analysis of various new fluorescent proteins would be important step towards the development of such fluorescent protein-based metal biosensors. Here, we first report the spectroscopic and structural analysis of the yellow fluorescent protein ZsYellow, following its metal-induced quenching. Spectroscopic analysis showed that ZsYellow exhibited a high degree of fluorescence quenching by Cu 2+ . During Cu 2+ -induced ZsYellow quenching, fluorescence emission was recovered by adding EDTA. The crystal structure of ZsYellow soaked in Cu 2+ solution was determined at a 2.6 Å resolution. The electron density map did not indicate the presence of Cu 2+ around the chromophore or the β-barrel surface, which resulted in fluorescence quenching without Cu 2+ binding to specific site in ZsYellow. Based on these results, we propose the fluorescence quenching to occur in a distance-dependent manner between the metal and the fluorescent protein, when these components get to a closer vicinity at higher metal concentrations. Our results provide useful insights for future development of fluorescent protein-based metal biosensors.


  • Organizational Affiliation
    • Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Korea.

Macromolecule Content 

  • Total Structure Weight: 52.87 kDa 
  • Atom Count: 3,658 
  • Modeled Residue Count: 449 
  • Deposited Residue Count: 464 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GFP-like fluorescent chromoprotein FP538A [auth C],
C [auth D]
68Zoanthus sp.Mutation(s): 0 
UniProt
Find proteins for Q9U6Y4 (Zoanthus sp.)
Explore Q9U6Y4 
Go to UniProtKB:  Q9U6Y4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9U6Y4
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
GFP-like fluorescent chromoprotein FP538B [auth A],
D [auth B]
164Zoanthus sp.Mutation(s): 2 
UniProt
Find proteins for Q9U6Y4 (Zoanthus sp.)
Explore Q9U6Y4 
Go to UniProtKB:  Q9U6Y4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9U6Y4
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
NFA
Query on NFA
A [auth C],
C [auth D]
L-PEPTIDE LINKINGC9 H12 N2 OPHE
CH7
Query on CH7
B [auth A],
D [auth B]
L-PEPTIDE LINKINGC17 H17 N3 O4LYS, TYR, GLY

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.215 (Depositor), 0.215 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.638α = 90
b = 72.929β = 90
c = 124.189γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data

  • Released Date: 2020-01-22 
  • Deposition Author(s): Nam, K.H.

Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic OfNRF-2017R1D1A1B03033087

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-22
    Type: Initial release
  • Version 1.1: 2020-07-29
    Changes: Database references
  • Version 1.2: 2020-10-14
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Database references, Refinement description
  • Version 2.0: 2026-03-18
    Changes: Polymer sequence, Structure summary