5LK4 | pdb_00005lk4

Structure of the Red Fluorescent Protein mScarlet at pH 7.8

• PDB DOI: https://doi.org/10.2210/pdb5LK4/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Discosoma sp.
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-07-20 Released: 2016-12-07 
• Deposition Author(s): Aumonier, S., Gotthard, G., Royant, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 
  0.167 (Depositor), 0.167 (DCC) 
• R-Value Work: 
  0.137 (Depositor), 0.136 (DCC) 
• R-Value Observed: 
  0.138 (Depositor) 

Starting Model: experimental

Literature

mScarlet: a bright monomeric red fluorescent protein for cellular imaging.

Bindels, D.S., Haarbosch, L., van Weeren, L., Postma, M., Wiese, K.E., Mastop, M., Aumonier, S., Gotthard, G., Royant, A., Hink, M.A., Gadella, T.W.

(2017) Nat Methods 14: 53-56

• PubMed: 27869816 
• DOI: https://doi.org/10.1038/nmeth.4074
• Primary Citation Related Structures: 
  5LK4


• PubMed Abstract: 
  

  We report the engineering of mScarlet, a truly monomeric red fluorescent protein with record brightness, quantum yield (70%) and fluorescence lifetime (3.9 ns). We developed mScarlet starting with a consensus synthetic template and using improved spectroscopic screening techniques; mScarlet's crystal structure reveals a planar and rigidified chromophore. mScarlet outperforms existing red fluorescent proteins as a fusion tag, and it is especially useful as a Förster resonance energy transfer (FRET) acceptor in ratiometric imaging.

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Organizational Affiliation: 
• Section of Molecular Cytology and van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands.
European Synchrotron Radiation Facility, Grenoble, France.
Institut de Biologie Structurale, Université Grenoble Alpes, CNRS, CEA, Grenoble, F-38044, France.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 25.89 kDa 
• Atom Count: 2,128 
• Modeled Residue Count: 217 
• Deposited Residue Count: 217 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mScarlet	A	217	Discosoma sp.	Mutation(s): 40
UniProt
Find proteins for Q9U6Y8 (Discosoma sp.) Explore Q9U6Y8  Go to UniProtKB:  Q9U6Y8

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	B [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE	D [auth A], E [auth A], F [auth A], G [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	H [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4	C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NRQ	A	L-PEPTIDE LINKING	C16 H17 N3 O4 S		MET, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free:  0.167 (Depositor), 0.167 (DCC) 
• R-Value Work:  0.137 (Depositor), 0.136 (DCC) 
• R-Value Observed: 0.138 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.2	α = 90
b = 35.64	β = 109.69
c = 86.01	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-07 
Deposition Author(s): Aumonier, S., Gotthard, G., Royant, A.

Revision History  

• Version 1.0: 2016-12-07
  Type: Initial release
  
• Version 1.1: 2017-01-11
  Changes: Database references
• Version 2.0: 2022-09-14
  Changes: Database references, Non-polymer description, Structure summary
• Version 2.1: 2024-01-31
  Changes: Data collection, Refinement description
• Version 3.0: 2026-03-18
  Changes: Polymer sequence, Structure summary