7DNA

Photocleavable Fluorescent Protein in green and red form

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

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This is version 2.0 of the entry. See complete history. 


Literature

Photocleavable proteins that undergo fast and efficient dissociation.

Lu, X., Wen, Y., Zhang, S., Zhang, W., Chen, Y., Shen, Y., Lemieux, M.J., Campbell, R.E.

(2021) Chem Sci 12: 9658-9672

  • DOI: https://doi.org/10.1039/d1sc01059j
  • Primary Citation of Related Structures:  
    7DMX, 7DNA, 7DNB

  • PubMed Abstract: 

    • Photocleavable molecules can enable the light-dependent modulation of biomolecular activities with high spatiotemporal precision. We have previously reported a photocleavable protein (PhoCl1) that, uniquely, is a fully genetically encoded photocleavable molecule that can be introduced into cells in the form of its corresponding gene to enable optogenetic control of biomolecular activities ...

    Photocleavable molecules can enable the light-dependent modulation of biomolecular activities with high spatiotemporal precision. We have previously reported a photocleavable protein (PhoCl1) that, uniquely, is a fully genetically encoded photocleavable molecule that can be introduced into cells in the form of its corresponding gene to enable optogenetic control of biomolecular activities. However, the first generation PhoCl1 exhibited a relatively slow rate of dissociation, potentially limiting its utility. Here, we report the X-ray crystal structures of the PhoCl1 green state, red state, and cleaved empty barrel. Molecular dynamics (MD) simulations were performed to provide insight into the precise dissociation mechanism. Using structure-guided engineering and directed evolution, we have developed PhoCl2c with higher contrast ratio and PhoCl2f with faster dissociation. We characterized the performance of these new variants as purified proteins and in cultured cells. Our results demonstrate that PhoCl2 variants exhibit faster and more efficient dissociation, which should enable improved optogenetic manipulations of protein localization and protein-protein interactions in living cells.

    Organizational Affiliation: 

    Department of Chemistry, The University of Tokyo Tokyo 113-0033 Japan.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Green-to-red photoconvertible GFP-like proteinA,
B,
C [auth D],
F [auth K]		240Aequorea victoriaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Green-to-red photoconvertible GFP-like proteinD [auth F],
E [auth I]		240Aequorea victoriaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NFA
Query on NFA
Download Ideal Coordinates CCD File 
G [auth F],
H [auth I]		PHENYLALANINE AMIDE
C9 H12 N2 O
OBSIQMZKFXFYLV-QMMMGPOBSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CR8
Query on CR8		A,
B,
C [auth D],
F [auth K]		L-PEPTIDE LINKINGC17 H16 N5 O4HIS, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.93α = 92.46
b = 72.49β = 97.31
c = 126.55γ = 92.5
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31870132

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-27
    Type: Initial release
  • Version 1.1: 2021-06-16
    Changes: Database references
  • Version 1.2: 2022-02-23
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.0: 2023-04-05
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Polymer sequence, Source and taxonomy, Structure summary