7UGS | pdb_00007ugs

Crystal structure of monomeric hyperfolder YFP (K206V mutant)

• PDB DOI: https://doi.org/10.2210/pdb7UGS/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Aequorea victoria
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-03-25 Released: 2022-10-26 
• Deposition Author(s): Campbell, B.C., Liu, C.F., Petsko, G.A.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 
  0.188 (Depositor), 0.188 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.152 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Starting Model: experimental

Literature

Chemically stable fluorescent proteins for advanced microscopy.

Campbell, B.C., Paez-Segala, M.G., Looger, L.L., Petsko, G.A., Liu, C.F.

(2022) Nat Methods 19: 1612-1621

• PubMed: 36344833 
• DOI: https://doi.org/10.1038/s41592-022-01660-7
• Primary Citation Related Structures: 
  7UGR, 7UGS, 7UGT


• PubMed Abstract: 
  

  We report the rational engineering of a remarkably stable yellow fluorescent protein (YFP), 'hyperfolder YFP' (hfYFP), that withstands chaotropic conditions that denature most biological structures within seconds, including superfolder green fluorescent protein (GFP). hfYFP contains no cysteines, is chloride insensitive and tolerates aldehyde and osmium tetroxide fixation better than common fluorescent proteins, enabling its use in expansion and electron microscopies. We solved crystal structures of hfYFP (to 1.7-Å resolution), a monomeric variant, monomeric hyperfolder YFP (1.6 Å) and an mGreenLantern mutant (1.2 Å), and then rationally engineered highly stable 405-nm-excitable GFPs, large Stokes shift (LSS) monomeric GFP (LSSmGFP) and LSSA12 from these structures. Lastly, we directly exploited the chemical stability of hfYFP and LSSmGFP by devising a fluorescence-assisted protein purification strategy enabling all steps of denaturing affinity chromatography to be visualized using ultraviolet or blue light. hfYFP and LSSmGFP represent a new generation of robustly stable fluorescent proteins developed for advanced biotechnological applications.

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Organizational Affiliation: 
• Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine, New York, NY, USA. [e-mail].
Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA. [e-mail].
Department of Neurosciences, University of California, San Diego, San Diego, CA, USA. [e-mail].
Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
Howard Hughes Medical Institute, Department of Neurosciences, University of California, San Diego, CA, USA.
Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine, New York, NY, USA.
Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
Ann Romney Institute for Neurologic Diseases, Department of Neurology, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, USA.
MeiraGTx, New York, NY, USA.

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: 26.95 kDa 
• Atom Count: 2,061 
• Modeled Residue Count: 227 
• Deposited Residue Count: 237 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hyperfolder yellow fluorescent protein	A	237	Aequorea victoria	Mutation(s): 0
UniProt
Find proteins for A0A059PIR9 (Aequorea victoria) Explore A0A059PIR9  Go to UniProtKB:  A0A059PIR9

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CR2	A	L-PEPTIDE LINKING	C13 H13 N3 O4		GLY, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free:  0.188 (Depositor), 0.188 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.152 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.347	α = 90
b = 66.659	β = 90
c = 142.465	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-10-26 
Deposition Author(s): Campbell, B.C., Liu, C.F., Petsko, G.A.

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Funding Organization	Location	Grant Number
Other private	United States	--

Revision History  

• Version 1.0: 2022-10-26
  Type: Initial release
  
• Version 1.1: 2022-11-16
  Changes: Database references
• Version 1.2: 2022-11-23
  Changes: Database references
• Version 1.3: 2022-12-14
  Changes: Database references
• Version 1.4: 2023-10-25
  Changes: Data collection, Refinement description
• Version 1.5: 2023-11-15
  Changes: Data collection
• Version 1.6: 2024-11-13
  Changes: Structure summary
• Version 2.0: 2026-03-18
  Changes: Polymer sequence