6GP0 | pdb_00006gp0

Structure of mEos4b in the red fluorescent state

PDB DOI: https://doi.org/10.2210/pdb6GP0/pdb

Classification: FLUORESCENT PROTEIN
Organism(s): Lobophyllia hemprichii
Expression System: Escherichia coli BL21(DE3)
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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.190 (Depositor), 0.190 (DCC)
R-Value Work:
0.154 (Depositor), 0.154 (DCC)
R-Value Observed:
0.155 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 4.0 of the entry. See complete history.

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 Search on PubMed
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.

Organizational Affiliation

Department of Chemistry, KU Leuven, Heverlee, Belgium.

Macromolecule Content

Total Structure Weight: 29.55 kDa
Atom Count: 2,304
Modeled Residue Count: 224
Deposited Residue Count: 259
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green to red photoconvertible GFP-like protein EosFP	A	257	Lobophyllia hemprichii	Mutation(s): 1
UniProt
Find proteins for Q5S6Z9 (Lobophyllia hemprichii) Explore Q5S6Z9 Go to UniProtKB: Q5S6Z9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5S6Z9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
5SQ Query on 5SQ	A	L-PEPTIDE LINKING	C₁₇ H₁₇ N₅ O₄		HIS, TYR, GLY
NFA Query on NFA	A	L-PEPTIDE LINKING	C₉ H₁₂ N₂ O		PHE

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.190 (Depositor), 0.190 (DCC)
R-Value Work: 0.154 (Depositor), 0.154 (DCC)
R-Value Observed: 0.155 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.61	α = 90
b = 57.9	β = 90
c = 102.64	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-05-22

Deposition Author(s):

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

Revision History (Full details and data files)

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: 2021-10-13
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, 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 4.0: 2025-07-16
Changes: Advisory, Atomic model, Database references, Derived calculations, Structure summary