6H01

Crystal structure of a domain-swapped dark-state sfGFP containing the unnatural amino acid ortho-nitrobenzyl-tyrosine (ONBY) at residue 66


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of a domain-swapped photoactivatable sfGFP variant provides evidence for GFP folding pathway.

Kesgin-Schaefer, S.Heidemann, J.Puchert, A.Koelbel, K.Yorke, B.A.Huse, N.Pearson, A.R.Uetrecht, C.Tidow, H.

(2019) FEBS J 286: 2329-2340

  • DOI: 10.1111/febs.14797
  • Primary Citation of Related Structures:  
    6H01

  • PubMed Abstract: 
  • Photoactivatable fluorescent proteins (PA-FPs) are a powerful non-invasive tool in high-resolution live-cell imaging. They can be converted from an inactive to an active form by light, enabling the spatial and temporal trafficking of proteins and cel ...

    Photoactivatable fluorescent proteins (PA-FPs) are a powerful non-invasive tool in high-resolution live-cell imaging. They can be converted from an inactive to an active form by light, enabling the spatial and temporal trafficking of proteins and cell dynamics. PA-FPs have been previously generated by mutating selected residues in the chromophore or in its close proximity. A new strategy to generate PA-FPs is the genetic incorporation of unnatural amino acids (UAAs) containing photocaged groups using unique suppressor tRNA/aminoacyl-tRNA synthetase pairs. We set out to develop a photoactivatable GFP variant suitable for time-resolved structural studies. Here, we report the crystal structure of superfolder GFP (sfGFP) containing the UAA ortho-nitrobenzyl-tyrosine (ONBY) at position 66 and its spectroscopic characterization. Surprisingly, the crystal structure (to 2.7 Å resolution) reveals a dimeric domain-swapped arrangement of sfGFP66ONBY with residues 1-142 of one molecule associating with residues 148-234 from another molecule. This unusual domain-swapped structure supports a previously postulated GFP folding pathway that proceeds via an equilibrium intermediate.


    Organizational Affiliation

    Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Green fluorescent proteinABCD264Aequorea victoriaMutation(s): 1 
Gene Names: gfp
Find proteins for A0A059PIQ0 (Aequorea victoria)
Explore A0A059PIQ0 
Go to UniProtKB:  A0A059PIQ0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FHE
Query on FHE
A,B,C,DL-PEPTIDE LINKINGC22 H20 N4 O7THR, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 155.324α = 90
b = 155.324β = 90
c = 161.977γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyDFG EXC 1074

Revision History 

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-06-26
    Changes: Data collection, Database references