5LTP | pdb_00005ltp

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: 1.70 Å
  • R-Value Free: 
    0.211 (Depositor), 0.216 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5LTP

This is version 2.0 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: https://doi.org/10.1107/S2059798316018623
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 184.7 kDa 
  • Atom Count: 11,949 
  • Modeled Residue Count: 1,338 
  • Deposited Residue Count: 1,614 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
mNeonGreen
A, B, C, D, E
A, B, C, D, E, F
269Branchiostoma lanceolatumMutation(s): 0 
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

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FLC

Query on FLC



Download:Ideal Coordinates CCD File
H [auth A],
I [auth A],
K [auth B]
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
CL

Query on CL



Download:Ideal Coordinates CCD File
G [auth A]
J [auth B]
L [auth C]
M [auth D]
N [auth E]
G [auth A],
J [auth B],
L [auth C],
M [auth D],
N [auth E],
O [auth F]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CR2
Query on CR2
A, B, C, D, E
A, B, C, D, E, F
L-PEPTIDE LINKINGC13 H13 N3 O4GLY, TYR, GLY

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.211 (Depositor), 0.216 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.87α = 90
b = 127.6β = 90
c = 146.84γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-21
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-10-09
    Changes: Structure summary
  • Version 2.0: 2026-03-18
    Changes: Polymer sequence