6GOY | pdb_00006goy

Structure of mEos4b in the green fluorescent state

• PDB DOI: https://doi.org/10.2210/pdb6GOY/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Lobophyllia hemprichii
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-06-04 Released: 2019-05-22 
• Deposition Author(s): De Zitter, E., Adam, V., Byrdin, M., Van Meervelt, L., Dedecker, P., Bourgeois, D.
• Funding Organization(s): Research Foundation - Flanders, Grenoble Instruct-ERIC Center (ISBG), FRISBI, GRAL

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.204 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

Mechanistic investigation of mEos4b reveals a strategy to reduce track interruptions in sptPALM.

De Zitter, E., Thedie, D., Monkemoller, V., Hugelier, S., Beaudouin, J., Adam, V., Byrdin, M., Van Meervelt, L., Dedecker, P., Bourgeois, D.

(2019) Nat Methods 16: 707-710

• PubMed: 31285624 
• DOI: https://doi.org/10.1038/s41592-019-0462-3
• Primary Citation Related Structures: 
  6GOY, 6GP0, 6GP1


• PubMed Abstract: 
  

  Green-to-red photoconvertible fluorescent proteins repeatedly enter dark states, causing interrupted tracks in single-particle-tracking localization microscopy (sptPALM). We identified a long-lived dark state in photoconverted mEos4b that results from isomerization of the chromophore and efficiently absorbs cyan light. Addition of weak 488-nm light swiftly reverts this dark state to the fluorescent state. This strategy largely eliminates slow blinking and enables the recording of longer tracks in sptPALM with minimum effort.

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Organizational Affiliation: 
• Department of Chemistry, KU Leuven, Heverlee, Belgium.
University Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France.
Department of Chemistry, KU Leuven, Heverlee, Belgium. [e-mail].
University Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 29.93 kDa 
• Atom Count: 2,192 
• Modeled Residue Count: 221 
• Deposited Residue Count: 257 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green to red photoconvertible GFP-like protein EosFP	A	257	Lobophyllia hemprichii	Mutation(s): 14
UniProt
Find proteins for Q5S6Z9 (Lobophyllia hemprichii) Explore Q5S6Z9  Go to UniProtKB:  Q5S6Z9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	B [auth A], C [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
5SQ	A	L-PEPTIDE LINKING	C17 H17 N5 O4		HIS, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.204 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.6	α = 90
b = 58.09	β = 90
c = 103.27	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-05-22 
Deposition Author(s): De Zitter, E., Adam, V., Byrdin, M., Van Meervelt, L., Dedecker, P., Bourgeois, D.

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Funding Organization	Location	Grant Number
Research Foundation - Flanders	Belgium	--
Grenoble Instruct-ERIC Center (ISBG)	France	UMS 3518 CNRS-CEA-UGA-EMBL
FRISBI	France	ANR-10-INBS-05-02
GRAL	France	ANR-10-LABX-49-01

Revision History  

• Version 1.0: 2019-05-22
  Type: Initial release
  
• Version 1.1: 2019-07-17
  Changes: Data collection, Database references
• Version 1.2: 2019-08-07
  Changes: Data collection, Database references
• Version 2.0: 2021-09-01
  Changes: Atomic model, Author supporting evidence, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
• Version 3.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations
• Version 3.1: 2024-01-17
  Changes: Refinement description
• Version 3.2: 2024-10-23
  Changes: Structure summary