5LTQ

Structure of the Yellow Fluorescent Protein lanYFP from Branchiostoma lanceolatum at pH 7.5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


This is version 1.1 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:  
    5LTP, 5LTQ, 5LTR

  • 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 particularly bright oligomeric fluorescent proteins such as the tetrameric yellow fluorescent protein lanYFP from Branchiostoma lanceolatum ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Green fluorescent protein blFP-Y3267Branchiostoma lanceolatumMutation(s): 3 
Gene Names: blFP-Y3
UniProt
Find proteins for B1PNC0 (Branchiostoma lanceolatum)
Explore B1PNC0 
Go to UniProtKB:  B1PNC0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB1PNC0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CR2
Query on CR2
A,
B [auth D],
C [auth B],
D [auth C],
E,
A,
B [auth D],
C [auth B],
D [auth C],
E,
F [auth H],
G [auth F],
H [auth G],
I,
J [auth L],
K [auth J],
L [auth K],
M,
N [auth P],
O [auth N],
P [auth O]
L-PEPTIDE LINKINGC13 H13 N3 O4GLY, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.66α = 90
b = 197.16β = 90.45
c = 115.09γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-07
    Type: Initial release
  • Version 1.1: 2016-12-21
    Changes: Database references