5JZK | pdb_00005jzk

The Structure of Ultra Stable Green Fluorescent Protein

• PDB DOI: https://doi.org/10.2210/pdb5JZK/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Aequorea victoria
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-05-17 Released: 2017-12-06 
• Deposition Author(s): Yong, K.J., Gunn, N.J., Scott, D.J., Griffin, M.D.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.176 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.142 (Depositor), 0.154 (DCC) 
• R-Value Observed: 
  0.144 (Depositor) 

Starting Model: experimental

Literature

A Novel Ultra-Stable, Monomeric Green Fluorescent Protein For Direct Volumetric Imaging of Whole Organs Using CLARITY.

Scott, D.J., Gunn, N.J., Yong, K.J., Wimmer, V.C., Veldhuis, N.A., Challis, L.M., Haidar, M., Petrou, S., Bathgate, R.A.D., Griffin, M.D.W.

(2018) Sci Rep 8: 667-667

• PubMed: 29330459 
• DOI: https://doi.org/10.1038/s41598-017-18045-y
• Primary Citation Related Structures: 
  5JZK, 5JZL


• PubMed Abstract: 
  

  Recent advances in thick tissue clearing are enabling high resolution, volumetric fluorescence imaging of complex cellular networks. Fluorescent proteins (FPs) such as GFP, however, can be inactivated by the denaturing chemicals used to remove lipids in some tissue clearing methods. Here, we solved the crystal structure of a recently engineered ultra-stable GFP (usGFP) and propose that the two stabilising mutations, Q69L and N164Y, act to improve hydrophobic packing in the core of the protein and facilitate hydrogen bonding networks at the surface, respectively. usGFP was found to dimerise strongly, which is not desirable for some applications. A point mutation at the dimer interface, F223D, generated monomeric usGFP (muGFP). Neurons in whole mouse brains were virally transduced with either EGFP or muGFP and subjected to Clear Lipid-exchanged Acrylamide-hybridized Rigid Imaging/Immunostaining/In situ hybridization-compatible Tissue-hYdrogel (CLARITY) clearing. muGFP fluorescence was retained after CLARITY whereas EGFP fluorescence was highly attenuated, thus demonstrating muGFP is a novel FP suitable for applications where high fluorescence stability and minimal self-association are required.

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Organizational Affiliation: 
• The Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, 3052, Australia. [e-mail].
Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, 3010, Australia. [e-mail].
The Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, 3052, Australia.
IBM Research, Southbank, Victoria, 3006, Australia.
Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, 3010, Australia.
Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia.
ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash University, Parkville, Victoria, 3052, Australia.
Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, 3010, Australia. [e-mail].
Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 56.71 kDa 
• Atom Count: 4,175 
• Modeled Residue Count: 470 
• Deposited Residue Count: 494 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein	A, B	247	Aequorea victoria	Mutation(s): 1  Gene Names: gfp
UniProt
Find proteins for P42212 (Aequorea victoria) Explore P42212  Go to UniProtKB:  P42212

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	E [auth A], J [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NO3	C [auth A], D [auth A], G [auth B], H [auth B]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CRO	A, B	L-PEPTIDE LINKING	C15 H17 N3 O5		THR, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.176 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.142 (Depositor), 0.154 (DCC) 
• R-Value Observed: 0.144 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.182	α = 90
b = 137.182	β = 90
c = 147.647	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-12-06 
Deposition Author(s): Yong, K.J., Gunn, N.J., Scott, D.J., Griffin, M.D.W.

Revision History  

• Version 1.0: 2017-12-06
  Type: Initial release
  
• Version 1.1: 2018-12-19
  Changes: Data collection, Database references
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection
• Version 1.4: 2024-10-30
  Changes: Structure summary
• Version 2.0: 2026-03-18
  Changes: Polymer sequence