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 1.2 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: https://doi.org/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. 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
MoleculeChains Sequence 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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth J]
BA [auth K]
CA [auth M]
DA [auth P]
EA [auth N]
AA [auth J],
BA [auth K],
CA [auth M],
DA [auth P],
EA [auth N],
FA [auth O],
Q [auth A],
R [auth D],
S [auth B],
T [auth C],
U [auth E],
V [auth H],
W [auth F],
X [auth G],
Y [auth I],
Z [auth L]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D 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
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description