4PFE | pdb_00004pfe

Crystal structure of vsfGFP-0

• PDB DOI: https://doi.org/10.2210/pdb4PFE/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Aequorea victoria, Vicugna pacos
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-04-29 Released: 2015-06-24 
• Deposition Author(s): Jauch, R., Chen, S.L.
• Funding Organization(s): National Research Foundation, Agency for Science, Technology, and Research/Genome Institute of Singapore

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.255 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Rational Structure-Based Design of Bright GFP-Based Complexes with Tunable Dimerization.

Eshaghi, M., Sun, G., Gruter, A., Lim, C.L., Chee, Y.C., Jung, G., Jauch, R., Wohland, T., Chen, S.L.

(2015) Angew Chem Int Ed Engl 54: 13952-13956

• PubMed: 26447926 
• DOI: https://doi.org/10.1002/anie.201506686
• Primary Citation of Related Structures:  
  4PFE


• PubMed Abstract: 
  

  Fluorescent proteins are transformative tools; thus, any brightness increase is a welcome improvement. We invented the "vGFP strategy" based on structural analysis of GFP bound to a single-domain antibody, predicting tunable dimerization, enhanced brightness (ca. 50%), and improved pH resistance. We verified all of these predictions using biochemistry, crystallography, and single-molecule studies. We applied the vsfGFP proteins in three diverse scenarios: single-step immunofluorescence in vitro (3× brighter due to dimerization); expression in bacteria and human cells in vivo (1.5× brighter); and protein fusions showing better pH resistance in human cells in vivo. The vGFP strategy thus allows upgrading of existing applications, is applicable to other fluorescent proteins, and suggests a method for tuning dimerization of arbitrary proteins and optimizing protein properties in general.

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Organizational Affiliation: 
• National University of Singapore, Department of Medicine, Yong Loo Lin School of Medicine, 1E Kent Ridge Road, NUHS Tower Block, Level 10, Singapore 119074 (Singapore).
National University of Singapore, Departments of Chemistry and Biological Sciences and Center for Bio-Imaging Sciences, Singapore 117557 (Singapore).
Saarland University, 66123 Saarbrücken (Germany).
Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530 (China).
National University of Singapore, Department of Medicine, Yong Loo Lin School of Medicine, 1E Kent Ridge Road, NUHS Tower Block, Level 10, Singapore 119074 (Singapore). [e-mail].
Genome Institute of Singapore, Infectious Diseases Group, 60 Biopolis Street, Genome, #02-01, Singapore 138672 (Singapore). [e-mail].

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 77.12 kDa 
• Atom Count: 5,555 
• Modeled Residue Count: 684 
• Deposited Residue Count: 686 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein	A, B	343	Aequorea victoria, Vicugna pacos This entity is chimeric	Mutation(s): 12  Gene Names: GFP
UniProt
Find proteins for P42212 (Aequorea victoria) Explore P42212  Go to UniProtKB:  P42212

Small Molecules

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: 2.60 Å
• R-Value Free:  0.255 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.426	α = 90
b = 83.426	β = 90
c = 228.691	γ = 90

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-06-24 
Deposition Author(s): Jauch, R., Chen, S.L.

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Funding Organization	Location	Grant Number
National Research Foundation	Singapore	NRF-RF2010-10
Agency for Science, Technology, and Research/Genome Institute of Singapore	Singapore	--

Revision History  

• Version 1.0: 2015-06-24
  Type: Initial release
  
• Version 1.1: 2016-02-10
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection
• Version 1.4: 2024-11-06
  Changes: Structure summary