5LTP

Structure of the Yellow-Green Fluorescent Protein mNeonGreen from Branchiostoma lanceolatum at the acidic pH 4.5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural analysis of the bright monomeric yellow-green fluorescent protein mNeonGreen obtained by directed evolution.

Clavel, D.Gotthard, G.von Stetten, D.De Sanctis, D.Pasquier, H.Lambert, G.G.Shaner, N.C.Royant, A.

(2016) Acta Crystallogr D Struct Biol 72: 1298-1307

  • DOI: 10.1107/S2059798316018623
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Until recently, genes coding for homologues of the autofluorescent protein GFP had only been identified in marine organisms from the phyla Cnidaria and Arthropoda. New fluorescent-protein genes have now been found in the phylum Chordata, coding for p ...

    Until recently, genes coding for homologues of the autofluorescent protein GFP had only been identified in marine organisms from the phyla Cnidaria and Arthropoda. New fluorescent-protein genes have now been found in the phylum Chordata, coding for particularly bright oligomeric fluorescent proteins such as the tetrameric yellow fluorescent protein lanYFP from Branchiostoma lanceolatum. A successful monomerization attempt led to the development of the bright yellow-green fluorescent protein mNeonGreen. The structures of lanYFP and mNeonGreen have been determined and compared in order to rationalize the directed evolution process leading from a bright, tetrameric to a still bright, monomeric fluorescent protein. An unusual discolouration of crystals of mNeonGreen was observed after X-ray data collection, which was investigated using a combination of X-ray crystallography and UV-visible absorption and Raman spectroscopies, revealing the effects of specific radiation damage in the chromophore cavity. It is shown that X-rays rapidly lead to the protonation of the phenolate O atom of the chromophore and to the loss of its planarity at the methylene bridge.


    Organizational Affiliation

    Université Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38044 Grenoble, France.,European Synchrotron Radiation Facility, F-38043 Grenoble, France.,CNRS, Laboratoire de Chimie Physique, UMR 8000 and Université Paris-Sud, F-91405 Orsay, France.,Department of Photobiology and Bioimaging, The Scintillon Institute, San Diego, California, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
mNeonGreen
A, B, C, D, E, F
271Branchiostoma lanceolatumMutation(s): 0 
Gene Names: blFP-Y3
Find proteins for A0A1S4NYF2 (Branchiostoma lanceolatum)
Go to UniProtKB:  A0A1S4NYF2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C, D, E, F
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
FLC
Query on FLC

Download SDF File 
Download CCD File 
A, B
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CR2
Query on CR2
A, B, C, D, E, F
L-PEPTIDE LINKINGC13 H13 N3 O4GLY, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 75.870α = 90.00
b = 127.600β = 90.00
c = 146.840γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-12-21
    Type: Initial release