7Z7O | pdb_00007z7o

Structure of the fluorescent protein NeonCyan0.95 at pH 7.5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 
    0.186 (Depositor), 0.172 (DCC) 
  • R-Value Work: 
    0.163 (Depositor), 0.154 (DCC) 
  • R-Value Observed: 
    0.164 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7Z7O

This is version 2.2 of the entry. See complete history

Literature

Cyan fluorescent proteins derived from mNeonGreen.

Zarowny, L.Clavel, D.Johannson, R.Duarte, K.Depernet, H.Dupuy, J.Baker, H.Brown, A.Royant, A.Campbell, R.E.

(2022) Protein Eng Des Sel 35

  • DOI: https://doi.org/10.1093/protein/gzac004
  • Primary Citation Related Structures: 
    7Z7O, 7Z7P, 7Z7Q

  • PubMed Abstract: 

    mNeonGreen, an engineered green fluorescent protein (GFP) derived from lancelet, is one of the most brightly fluorescent homologs of Aequorea victoria jellyfish GFP (avGFP) yet reported. In this work, we investigated whether this bright fluorescence might be retained in homologs of mNeonGreen with modified chromophore structures and altered fluorescent hues. We found mNeonGreen to be generally less tolerant than avGFP to chromophore modification by substitution of the key chromophore-forming tyrosine residue with other aromatic amino acids. However, we were ultimately successful in creating a variant, designated as NeonCyan1, with a tryptophan-derived cyan fluorescent protein (CFP)-type chromophore, and two additional mutants with distinct spectral hues. Structural, computational, and photophysical characterization of NeonCyan1 and its variants provided insight into the factors that control the fluorescence emission color. Though not recommended as replacements for contemporary CFP variants, we demonstrate that NeonCyan1 variants are potentially suitable for live cell imaging applications.


  • Organizational Affiliation
    • Department of Chemistry, University of Alberta, Edmonton T6G 2G2, Canada.

Macromolecule Content 

  • Total Structure Weight: 106.44 kDa 
  • Atom Count: 7,596 
  • Modeled Residue Count: 891 
  • Deposited Residue Count: 936 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NeonCyan0.95
A, B, C, D
234Branchiostoma lanceolatumMutation(s): 29 
Gene Names: blFP-Y3
UniProt
Find proteins for A0A1S4NYF2 (Branchiostoma lanceolatum)
Explore A0A1S4NYF2 
Go to UniProtKB:  A0A1S4NYF2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S4NYF2
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
IO8
Query on IO8
A, B, C, D
L-PEPTIDE LINKINGC15 H14 N4 O3GLY, TRP, GLY

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free:  0.186 (Depositor), 0.172 (DCC) 
  • R-Value Work:  0.163 (Depositor), 0.154 (DCC) 
  • R-Value Observed: 0.164 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.852α = 89.95
b = 60.662β = 71.79
c = 67.074γ = 90.01
Software Package:
Software NamePurpose
autoPROCdata processing
XDSdata reduction
XDSdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-17-CE11-0013
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM109984

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-04
    Type: Initial release
  • Version 1.1: 2022-05-18
    Changes: Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations
  • Version 2.1: 2024-01-31
    Changes: Refinement description
  • Version 2.2: 2024-11-06
    Changes: Structure summary