5JVA | pdb_00005jva

1.95 angstrom crystal structure of TAGRFP-T

  • Classification: FLUORESCENT PROTEIN
  • Organism(s): synthetic construct
  • Mutation(s): No 

  • Deposited: 2016-05-11 Released: 2017-05-17 
  • Deposition Author(s): Hu, X.J.
  • Funding Organization(s): the National Natural Science Foundation of China,

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.230 (Depositor), 0.237 (DCC) 
  • R-Value Work: 
    0.181 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 2.0 of the entry. See complete history

Literature

The crystal structure of red fluorescent protein TagRFP-T reveals the mechanism of its superior photostability.

Liu, R.Liang, Q.N.Du, S.Q.Hu, X.J.Ding, Y.

(2016) Biochem Biophys Res Commun 477: 229-234

  • DOI: https://doi.org/10.1016/j.bbrc.2016.06.047
  • Primary Citation Related Structures: 
    5JVA

  • PubMed Abstract: 

    The red fluorescent protein variant TagRFP-T has greatly improved photostability over its parent molecule, TagRFP, but the underlying mechanism leading to this improvement is to date unknown. The 1.95 Å resolution crystallographic structure of TagRFP-T showed that its chromophore exists as a mixture of cis and trans coplanar isomers in roughly equal proportions. Interestingly, both isomers are able to fluoresce, a property that has never been observed in any other fluorescent protein. We propose a "circular restoration model" for TagRFP-T to explain its superior photostability: There are four co-existing chromophore states (cis/trans protonated/ionized state) that can be driven by light to transform from one state into another. This model also explains how TagRPF-T essentially eliminates the temporary dark state (reversible photobleaching).


  • Organizational Affiliation
    • Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China.

Macromolecule Content 

  • Total Structure Weight: 109.12 kDa 
  • Atom Count: 7,730 
  • Modeled Residue Count: 900 
  • Deposited Residue Count: 952 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TagRFP-T
A, B, C, D
238synthetic constructMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.230 (Depositor), 0.237 (DCC) 
  • R-Value Work:  0.181 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 162.21α = 90
b = 162.21β = 90
c = 76.15γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data

  • Released Date: 2017-05-17 
  • Deposition Author(s): Hu, X.J.
  • This entry supersedes: 3T6H

Funding OrganizationLocationGrant Number
the National Natural Science Foundation of China,China31470764

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-17
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2023-11-15
    Changes: Data collection
  • Version 1.3: 2024-04-03
    Changes: Derived calculations
  • Version 2.0: 2026-03-18
    Changes: Polymer sequence, Structure summary