9DVE | pdb_00009dve

X-ray crystal structure of Kohinoor reversibly switchable fluorescent protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.272 (Depositor), 0.272 (DCC) 
  • R-Value Work: 
    0.244 (Depositor), 0.245 (DCC) 
  • R-Value Observed: 
    0.246 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Ultrafast photophysics of a positive reversibly switchable fluorescent protein.

Fatima, A.He, Y.Iuliano, J.N.Greetham, G.M.Malakar, P.Hall, C.Woroniecka, H.A.Richardson, B.C.French, J.B.Lukacs, A.Tonge, P.J.Meech, S.R.

(2025) Chem Sci 16: 16955-16969

  • DOI: https://doi.org/10.1039/d5sc04491j
  • Primary Citation of Related Structures:  
    9DVE

  • PubMed Abstract: 

    Reversibly switchable fluorescent proteins (rsFPs) are essential tools in super-resolution imaging. The mechanism operating in the widely applied negative switching rsFPs has been studied in detail. Much less attention has been paid to the positive switching rsFP variants, which offer the potential benefit of emissive states that do not photoswitch during measurement. Here we probe photochemical mechanism in all three photoactive states of the positive switching rsFP Kohinoor using a combination of ultrafast transient absorption, to probe chromophore population dynamics, and time resolved infrared, to access both chromophore populations and their effect on the surrounding protein matrix. We establish that none of the photochemical reactions are simple rate processes with transient absorption and transient IR data characterised by a common two component relaxation mechanism. Transient IR measurements reveal instantaneous coupling between the electronically excited chromophore and its protein environment, indicating that coupling arises from electrostatic or H-bonded interactions. In both on- and off-switching states the early phase of the excited state dynamics involve an initial relaxation in the perturbed protein environment, which leads to an intermediate state from which chromophore isomerization occurs. This result suggests that the protein dynamics play an active role in steering the excited state reaction, which is in-turn consistent with the known key role of the protein environment in tuning FP photophysics. Identifying and modifying the interactions between chromophore and protein will provide a means to optimise rsFP performance and thus a basis for development of improved labels for super-resolution bioimaging.


  • Organizational Affiliation
    • School of Chemistry, University of East Anglia Norwich NR4 7TJ UK s.meech@uea.ac.uk.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kohinoor
A, B, C, D
226synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
E [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
GYC
Query on GYC
A, B, C, D
L-PEPTIDE LINKINGC14 H15 N3 O4 SCYS, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.272 (Depositor), 0.272 (DCC) 
  • R-Value Work:  0.244 (Depositor), 0.245 (DCC) 
  • R-Value Observed: 0.246 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.53α = 90
b = 73.628β = 115.86
c = 93.219γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States2042704
Department of Energy (DOE, United States)United StatesKP1605010
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP30GM133893

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-03
    Type: Initial release
  • Version 1.1: 2025-09-10
    Changes: Database references
  • Version 1.2: 2025-10-01
    Changes: Database references