8ILL

Crystal structure of a highly photostable and bright green fluorescent protein at pH5.6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.157 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

StayGold variants for molecular fusion and membrane-targeting applications.

Ando, R.Shimozono, S.Ago, H.Takagi, M.Sugiyama, M.Kurokawa, H.Hirano, M.Niino, Y.Ueno, G.Ishidate, F.Fujiwara, T.Okada, Y.Yamamoto, M.Miyawaki, A.

(2024) Nat Methods 21: 648-656

  • DOI: https://doi.org/10.1038/s41592-023-02085-6
  • Primary Citation of Related Structures:  
    8ILK, 8ILL

  • PubMed Abstract: 

    Although StayGold is a bright and highly photostable fluorescent protein, its propensity for obligate dimer formation may hinder applications in molecular fusion and membrane targeting. To attain monovalent as well as bright and photostable labeling, we engineered tandem dimers of StayGold to promote dispersibility. On the basis of the crystal structure of this fluorescent protein, we disrupted the dimerization to generate a monomeric variant that offers improved photostability and brightness compared to StayGold. We applied the new monovalent StayGold tools to live-cell imaging experiments using spinning-disk laser-scanning confocal microscopy or structured illumination microscopy. We achieved cell-wide, high-spatiotemporal resolution and sustained imaging of dynamic subcellular events, including the targeting of endogenous condensin I to mitotic chromosomes, the movement of the Golgi apparatus and its membranous derivatives along microtubule networks, the distribution of cortical filamentous actin and the remolding of cristae membranes within mobile mitochondria.


  • Organizational Affiliation

    Laboratory for Cell Function Dynamics, RIKEN Center for Brain Science, Wako-city, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
green fluorescent protein
A, B
222synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose
C
2N/A
Glycosylation Resources
GlyTouCan:  G92130SN
GlyCosmos:  G92130SN
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CR2
Query on CR2
A, B
L-PEPTIDE LINKINGC13 H13 N3 O4GLY, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.157 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.999α = 90
b = 133.999β = 90
c = 59.023γ = 120
Software Package:
Software NamePurpose
DIALSdata reduction
DIALSdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)JapanJP21am0101070
Japan Society for the Promotion of Science (JSPS)Japan21H05041
Japan Society for the Promotion of Science (JSPS)Japan15H05948
Japan Agency for Medical Research and Development (AMED)JapanJP15dm0207001

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-04
    Type: Initial release
  • Version 1.1: 2023-11-15
    Changes: Data collection
  • Version 1.2: 2024-04-17
    Changes: Database references
  • Version 1.3: 2024-04-24
    Changes: Database references
  • Version 1.4: 2024-11-20
    Changes: Structure summary