SSBD:database v3

387-Ando-StayGold

Project

Title
Super resolution cellular images using fluorescent-tags of StayGold variants
Description
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, the authors engineered tandem dimers of StayGold to promote dispersibility. On the basis of the crystal structure of this fluorescent protein, they disrupted the dimerization to generate a monomeric variant that offers improved photostability and brightness compared to StayGold. The authors applied the new monovalent StayGold tools to live-cell imaging experiments using spinning-disk laser-scanning confocal microscopy or structured illumination microscopy. They 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.
License
CC BY 4.0
Released at
Oct. 20, 2025, midnight
Updated at
Funding
This work was supported in part by Grant-in-Aid for Scientific Research (S) (21H05041 to A.M.), Grant-in-Aid for Innovative Areas: Resonance Bio (15H05948 to A.M.) and Information Physics of Living Matters (19H05794 and 19H05795 to Y.O.), Japan Science and Technology Agency Core Research for Evolutionary Science and Technology program, ‘Spatiotemporal dynamics of intracellular components’ (JPM JCR20E2 to Y.O.) and Moonshot R&D program ‘Realization of ultra-early disease prediction and intervention by 2050’ (JPM JMS2025-14 to Y.O.), Marine Biomass Innovation Project (NFRFT-2020-00452 to A.M.), the Brain Mapping by Integrated Neurotechnologies for Disease Studies from AMED (Brain/MINDS, JP15dm0207001 to A.M.), RIKEN Collaboration Seed Fund (to M.T. and R.A.) and Platform Project for Supporting Drug Discovery and Life Science Research (Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)) from AMED (JP21am0101070 to M.Y.).
# of image datasets
31

Papers

Papers
Paper information: 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. StayGold variants for molecular fusion and membrane-targeting applications. Nat Methods. 2024 Apr;21(4):648-656.,
Pubmed ID: 38036853,
PMCID: PMC11009113,
DOI: https://doi.org/10.1038/s41592-023-02085-6,
URL: https://pubmed.ncbi.nlm.nih.gov/38036853/

Contacts

Contacts
Atsushi Miyawaki (Contact) , Laboratory for Cell Function Dynamics, RIKEN Center for Brain Science , RIKEN
Ryoko Ando (Imaging contributor) , Laboratory for Cell Function Dynamics, RIKEN Center for Brain Science , RIKEN
Satoshi Shimozono (Imaging contributor) , Laboratory for Cell Function Dynamics, RIKEN Center for Brain Science , RIKEN
Masatoshi Takagi (Imaging contributor) , Cellular Dynamics Laboratory, RIKEN Cluster for Pioneering Research (CPR) , RIKEN
Mayu Sugiyama (Imaging contributor) , Laboratory for Cell Function Dynamics, RIKEN Center for Brain Science , RIKEN
Hiroshi Kurokawa (Imaging contributor) , Laboratory for Cell Function Dynamics, RIKEN Center for Brain Science , RIKEN
Fumiyoshi Ishidate (Imaging contributor) , Institute for Integrated Cell-Material Sciences (WPI-iCeMS) , Kyoto University
Takahiro Fujiwara (Imaging contributor) , Institute for Integrated Cell-Material Sciences (WPI-iCeMS) , Kyoto University
Yasushi Okada (Imaging contributor) , Laboratory for Cell Polarity Regulation, RIKEN Center for Biosystems Dynamics Research , RIKEN

Biosamples

Organisms
Chlorocebus pygerythrus (NCBI:txid60710)
Homo sapiens (NCBI:txid9606)
Strains

Cells

Cell lines
COS-7 cell
HeLa cell
HCT 116 cell

Ontologies

UBERON
cell (CL_0000000)
Anatomical entities
GO: Biological processes
cellular response to histamine (GO:0071420)
chromosome organization (GO:0051276)
negative regulation of actin filament polymerization (GO:0030837)
Golgi organization (GO:0007030)
GO: Cellular components
Golgi apparatus (GO:0005794)
mitochondrion (GO:0005739)
nucleus (GO:0005634)
actin cytoskeleton (GO:0015629)
chromosome (GO:0005694)
GO: Molecular functions

Genetics

Gene names
Protein names
Tubulin beta-1 chain (Q9H4B7)
Trans-Golgi network integral membrane protein 2 (O43493)
Golgin subfamily A member 2 (Q08379)
Golgin subfamily B member 1 (Q14789)
Condensin complex subunit 2 (Q15003)
Cytochrome c oxidase subunit 8A, mitochondrial (P10176)
Genetic methods
treatment (EFO_0000727)
gene knock in, CRISPR-Cas9 genome-editing technique (EFO_0004963)
transfection (EFO_0000726)
Protein tags
Alexa Fluor 647 (FBbi:00000447)
Probes
antibody (FBbi:00000401)
Oligo Primer
Genotype

Treatments

Reagent or Compound
Concentration
Fold Dilution
cytochalasin D (CHEBI:529996)
1 micromolar (UO_0000064)
latrunculin A (CHEBI:69136)
2 micromolar (UO_0000064)
cytochalasin D (CHEBI:529996)
1 micromolar (UO_0000064)
latrunculin A (CHEBI:69136)
2 micromolar (UO_0000064)
ionomycin (CHEBI:63954)
1 micromolar (UO_0000064)
ionomycin (CHEBI:63954)
1 micromolar (UO_0000064)

Imaging Methods

Dimensions
548x548x1x1x1000, 1024x1024x1x1x1000, 1600x1600x1x1x18, 512x512x26x3x1, 512x512x28x3x1, 1024x1024x1x1x2000, 512x512x1x3x1, 2048x2048x1x1x81, 404x404x1x1x40, 1024x1024x1x1x800, 512x512x34x3x1, 548x548x1x1x1500, 1024x1024x3x1x100, 512x512x1x3x1, 1024x1024x1x1x500, 1024x1024x1x2x1801, 512x512x1x3x1, 1024x1024x5x1x200, 512x512x1x3x1, 1024x1024x13x2x30, 512x512x27x3x1,
X scales
0.04 micrometer, 0.13 micrometer, NA, 0.1 micrometer, 0.03 micrometer,
Y scales
0.04 micrometer, 0.13 micrometer, NA, 0.1 micrometer, 0.03 micrometer,
Z scales
NA, 1 micrometer, 0.5 micrometer, 0.52 micrometeer,
T scales
1 minute, 1 second, NA, 0.31 second, 3.18 frames/second, 6.9 seconds, 0.11 second, 8.70 frames/second, 0.41 second, 2.41 frames/second, 0.4 seconds,
Channels
2 channel, 1 channel,
Microscopy types
spinning disk confocal microscopy (FBbi:00000253)
Detection methods
Visualization methods
Illumination methods
Sources of contrast
Contrast enhancing methods
Resolution enhancing methods
Imaged parameters
Sample preparation methods

Instruments

Body
Zeiss Elyra 7
Model
Light source
Detector
Objective
PlanApo ×63/1.46 NA oil
Filter set
Dichroic
Body
Olympus-Evident IX83
Model
Light source
Detector
Hamamatsu ORCA-Flash4.0 CL, USB
Objective
Olympus-Evident UPLAPO100XOHR
Filter set
Dichroic

Datasets

Dataset name
Organism
Gene / Protein
Dimensions
File size
SSBD:OMERO
Download
Fig4_chromosome
Homo sapiens (NCBI:txid9606)
NA / Condensin complex subunit 2 (Q15003)
1024x1024x1x2x1801, 512x512x1x3x1
7GB
zip
Video2_chromosome
Homo sapiens (NCBI:txid9606)
NA / Condensin complex subunit 2 (Q15003)
1024x1024x13x2x30
1.5GB
zip
ExtFig6a_chromosome_fast
Homo sapiens (NCBI:txid9606)
NA / Condensin complex subunit 2 (Q15003)
1024x1024x1x2x1801, 512x512x1x3x1
7GB
zip
ExtFig6b_mClover3
Homo sapiens (NCBI:txid9606)
NA / Condensin complex subunit 2 (Q15003)
404x404x1x1x40
13MB
zip
ExtFig6b_td5oxSG
Homo sapiens (NCBI:txid9606)
NA / Condensin complex subunit 2 (Q15003)
404x404x1x1x40
13MB
zip
Video5_GianCreg_1
Homo sapiens (NCBI:txid9606)
/ Golgin subfamily B member 1 (Q14789)
1024x1024x5x1x200, 512x512x1x3x1
2GB
zip
Video5_GianCreg_2
Homo sapiens (NCBI:txid9606)
/ Golgin subfamily B member 1 (Q14789)
1024x1024x5x1x200, 512x512x1x3x1
2GB
zip
Video6_GianCreg_Tub
Chlorocebus pygerythrus (NCBI:txid60710)
/ Golgin subfamily B member 1 (Q14789) / Tubulin beta-1 chain (Q9H4B7)
1024x1024x3x1x100, 512x512x1x3x1
600MB
zip
SupplFig16_GianCreg_Tub
Chlorocebus pygerythrus (NCBI:txid60710)
/ Golgin subfamily B member 1 (Q14789) / Tubulin beta-1 chain (Q9H4B7)
1600x1600x1x1x18
88MB
zip
ExtFig7a_GM130_1
Homo sapiens (NCBI:txid9606)
/ Golgin subfamily B member 1 (Q14789) / Golgin subfamily A member 2 (Q08379)
512x512x26x3x1
39MB
zip
ExtFig7a_GM130_2
Homo sapiens (NCBI:txid9606)
/ Golgin subfamily B member 1 (Q14789) / Golgin subfamily A member 2 (Q08379)
512x512x27x3x1
41MB
zip
ExtFig7a_GM130_3
Homo sapiens (NCBI:txid9606)
/ Golgin subfamily B member 1 (Q14789) / Golgin subfamily A member 2 (Q08379)
512x512x26x3x1
39MB
zip
ExtFig7b_Giantin_1
Homo sapiens (NCBI:txid9606)
/ Golgin subfamily B member 1 (Q14789)
512x512x27x3x1
41MB
zip
ExtFig7b_Giantin_2
Homo sapiens (NCBI:txid9606)
/ Golgin subfamily B member 1 (Q14789)
512x512x26x3x1
39MB
zip
ExtFig7b_Giantin_3
Homo sapiens (NCBI:txid9606)
/ Golgin subfamily B member 1 (Q14789)
512x512x28x3x1
42MB
zip
ExtFig7c_TGN46_1
Homo sapiens (NCBI:txid9606)
/ Golgin subfamily B member 1 (Q14789) / Trans-Golgi network integral membrane protein 2 (O43493)
512x512x26x3x1
39MB
zip
ExtFig7c_TGN46_2
Homo sapiens (NCBI:txid9606)
/ Golgin subfamily B member 1 (Q14789) / Trans-Golgi network integral membrane protein 2 (O43493)
512x512x27x3x1
41MB
zip
ExtFig7c_TGN46_3
Homo sapiens (NCBI:txid9606)
/ Golgin subfamily B member 1 (Q14789) / Trans-Golgi network integral membrane protein 2 (O43493)
512x512x34x3x1
51MB
zip
VIdeo7_Ftractin_1
Chlorocebus pygerythrus (NCBI:txid60710)
548x548x1x1x1000
859MB
zip
VIdeo7_Ftractin_2
Chlorocebus pygerythrus (NCBI:txid60710)
548x548x1x1x1500
573MB
zip
Video7_UtrCH_1
Chlorocebus pygerythrus (NCBI:txid60710)
548x548x1x1x1000
573MB
zip
Video7_UtrCH_2
Chlorocebus pygerythrus (NCBI:txid60710)
548x548x1x1x1000
573MB
zip
ExtFig8_Ftractin_CytD
Chlorocebus pygerythrus (NCBI:txid60710)
1024x1024x1x1x2000, 512x512x1x3x1
3.9GB
zip
ExtFig8_Ftractin_LatA
Chlorocebus pygerythrus (NCBI:txid60710)
1024x1024x1x1x2000, 512x512x1x3x1
3.9GB
zip
ExtFig8_UtrCH_CytD
Chlorocebus pygerythrus (NCBI:txid60710)
1024x1024x1x1x2000, 512x512x1x3x1
3.9GB
zip
ExtFig8_UtrCH_LatA
Chlorocebus pygerythrus (NCBI:txid60710)
1024x1024x1x1x2000, 512x512x1x3x1
3.9GB
zip
Fig5c_COX8a
Homo sapiens (NCBI:txid9606)
/ Cytochrome c oxidase subunit 8A, mitochondrial (P10176)
2048x2048x1x1x81
648MB
zip
Video10_COX8a
Homo sapiens (NCBI:txid9606)
/ Cytochrome c oxidase subunit 8A, mitochondrial (P10176)
1024x1024x1x1x1000
2GB
zip
Video11_COX8a
Homo sapiens (NCBI:txid9606)
/ Cytochrome c oxidase subunit 8A, mitochondrial (P10176)
1024x1024x1x1x500
1GB
zip
Video12_COX8a_reagent_1
Homo sapiens (NCBI:txid9606)
/ Cytochrome c oxidase subunit 8A, mitochondrial (P10176)
1024x1024x1x1x800
1.6GB
zip
Video12_COX8a_reagent_2
Homo sapiens (NCBI:txid9606)
/ Cytochrome c oxidase subunit 8A, mitochondrial (P10176)
1024x1024x1x1x800
1.6GB
zip