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. 2025 May 20;13:RP103486. doi: 10.7554/eLife.103486

Appendix 1—key resources table.

Reagent type (species) or resource Designation Source or reference Identifiers Additional information
Antibody Anti-histone H1.8 (Xenopus laevis) Rabbit polyclonal antibody Jenness et al., 2018 RU2130 1 µg/mL
Antibody Anti-histone H3T3ph mouse monoclonal antibody Kelly et al., 2008 16B2 1:5000 dilution
Antibody IRDye 680LT goat anti-rabbit IgG LI-COR 926–68021; RRID:AB_10706309 1:15,000 dilution
Antibody IR Dye 800CW goat anti-mouse IgG LI-COR 926–32210; RRID:AB_621842 1:10,000 dilution
Antibody Anti-histone NAP1 (Xenopus laevis) Rabbit polyclonal antibody Lorton et al., 2023 N/A 1:500 dilution
Antibody Anti-histone NPM2 (Xenopus laevis) Rabbit polyclonal antibody Lorton et al., 2023 N/A 1:500 dilution
Antibody Anti-rabbit IgG SIGMA I5006, RRID:AB_1163659
Antibody Anti-rabbit IgG (purified from pre-bleed sera) This work N/A
Antibody Cy3 AffiniPure F(ab')₂ Fragment Donkey Anti-Mouse IgG (H+L) Jackson ImmunoResearch 715-166-150, RRID:AB_2340816 1:500 dilution
Antibody Cy5 AffiniPure Donkey Anti-Rabbit IgG (H+L) Jackson ImmunoResearch 711-175-152, RRID:AB_2340607 1:500 dilution
Strain, strain background (E. coli) E. coli Rosetta (DE3) Novagen 70954–3
Strain, strain background (E. coli) E. coli BL21(DE3) Novagen 69450–3
Strain, strain background (E. coli) E. coli JM101 Agilent 200234
Biological sample (Xenopus laevis) Xenopus laevis sperm nuclei Nasco, Isolated from male Xenopus laevis LM00715 (male Xenopus laevis)
Biological sample (Xenopus laevis) Xenopus laevis egg Nasco, Laid by female Xenopus laevis LM00535 (female Xenopus laevis)
Biological sample (Xenopus laevis) Alexa594-labeled-tubulin Hyman et al., 1991; Isolated from bovine brain n/a
Chemical compound, drug Chorionic gonadotropin human Sigma CG10-1VL
Chemical compound, drug Pregnant Mare Serum Gonadotropin (PMSG) Prospec HOR-272
Chemical compound, drug Cycloheximide Sigma C-7698
Chemical compound, drug CaCl2 Sigma Aldrich C7902-500G
Peptide, recombinant protein Cyclin B Δ90 Glotzer et al., 1991 N/A
Chemical compound, drug Cysteine Sigma C7352-1KG
Chemical compound, drug PIPES Alfa Aesar A16090
Chemical compound, drug NaCl Millipore Sigma SX0420-5
Chemical compound, drug Glycerol Alfa Aesar 36646
Chemical compound, drug EGTA Sigma Aldrich E4378-250G
Chemical compound, drug MgCl2 Acros organic 197530010
Chemical compound, drug β-glycerophosphate Acros organic 410991000
Chemical compound, drug Sodium butyrate Aldrich 303410–100 G
Chemical compound, drug Formaldehyde Fisher bioreagents BP531-25
Chemical compound, drug HEPES Akron biotech AK1069-1000
Chemical compound, drug Sucrose Fisher chemical S5-3
Chemical compound, drug KCl Fisher chemical P217-3
Chemical compound, drug Spermidine Sigma S-2501
Chemical compound, drug Spermine Sigma S1141-5G
Chemical compound, drug cOmplete EDTA-free Protease Inhibitor Cocktail Roche 11873580001
Chemical compound, drug Leupeptin Millipore Sigma El8
Chemical compound, drug Pepstatin Sigma P5318-25MG
Chemical compound, drug Chymostatin Millipore Sigma El6
Peptide, recombinant protein RNaseA Thermo Scientific EN0531
Peptide, recombinant protein Proteinase K solution Roche 3115828001
Chemical compound, drug SYBR-safe Invitrogen S33102
Chemical compound, drug 4–20% gradient SDS-PAGE gel BioRad 4561096
Chemical compound, drug SYTO-60 Invitrogen S11342
Chemical compound, drug Tris Sigma T1503-5KG
Chemical compound, drug Glycine Sigma G7126-5KG
Chemical compound, drug Amicon Ultra centrifugal filter 100 K Millipore Sigma UFC510024
Chemical compound, drug Methanol Fisher chemical A452SK-4
Chemical compound, drug Tube-o-dialyzer 15 kDa G-Biosciences 786–618
Chemical compound, drug Amicon Ultra centrifugal filters 3 K Millipore Sigma UFC500324
Chemical compound, drug Coomassie Brilliant Blue G-250 Calbiochem 3340
Peptide, recombinant protein Xenopus laevis H2A, H2B, H3.2, H4 Zierhut et al., 2014 N/A
Chemical compound, drug Ni-NTA beads QIAGEN 30210
Chemical compound, drug Carbenicillin Alfa Aesar J61949
Chemical compound, drug Methanol Fisher chemical A452SK-4
Chemical compound, drug Trehalose Sigma T0167-100G
Chemical compound, drug 1,6,-hexanediol Alfa Aesar A12439
Peptide, recombinant protein MluI New England Biolabs R3198S
Peptide, recombinant protein AscI New England Biolabs R0558S
Peptide, recombinant protein XhoI New England Biolabs R0146S
Chemical compound, drug EZ-link Maleimide-PEG2-Biotin Thermo A39261
Chemical compound, drug Isopropyl-β-D-thiogalactopyranoside (IPTG) RPI research products I56000-25.0
Peptide, recombinant protein Mono-SPYtag-avidin tetramer This work
Peptide, recombinant protein Biotin-30 nm-SAH-SPYcatcher003 This work
Peptide, recombinant protein Biotin-60 nm-SAH-SPYcatcher003 This work
Peptide, recombinant protein Biotin-90 nm-SAH-SPYcatcher003 This work
Peptide, recombinant protein Biotin-3HB-SPYcatcher003 This work
Peptide, recombinant protein SPYtag-GFPenhancer-GGGGS4-LaG16 This work
Peptide, recombinant protein SPYtag-GFP enhancer nanobody This work
Peptide, recombinant protein SPYtag-LaG (llama antibody against GFP)–10 This work
Peptide, recombinant protein H1.8-GFP This work
Peptide, recombinant protein MNase This work
Peptide, recombinant protein HaeII New England Biolabs R0107S
Peptide, recombinant protein DraI New England Biolabs R0129S
Peptide, recombinant protein EcoRI New England Biolabs R3101S
Peptide, recombinant protein XbaI New England Biolabs R0145S
Peptide, recombinant protein Klenow fragment New England Biolabs M0212S
Chemical compound, drug biotin-14-dATP Jena Bioscience GmbH NU-835-BIO14-S
Chemical compound, drug Intercept TBS Blocking Buffer LI-COR Biosciences 927–60001
Chemical compound, drug nitrocellulose membrane Cytiva 10600000
Chemical compound, drug Protein-A coupled Dynabeads Thermo Fisher Scientific 10001D
Chemical compound, drug Hi-load Superdex200 16/600 column (Cytiva) Cytiva 28989335
Chemical compound, drug Hi-load Superdex75 16/600 column (Cytiva) Cytiva 28989333
Chemical compound, drug BS3 (bis(sulfosuccinimidyl)suberate) Thermo Fisher Scientific A39266
Chemical compound, drug 1 x PhosSTOP Roche 4906845001
Chemical compound, drug Absolute Mag streptavidin nano-magnetic beads CD bioparticles WHM-X047
Chemical compound, drug monolayer graphene grown on the copper foil Grolltex GRF23-L062−6x6
Chemical compound, drug polymethyl methacrylate Micro chem EL6
Chemical compound, drug Ammonium Persulfate Thermo Scientific AC401165000
Chemical compound, drug 2-butanone Thermo Scientific AA39119K7
Chemical compound, drug 2-propanol Fisher Scientific BP26184
Chemical compound, drug NucBlue Fixed Cell ReadyProbes Reagent Thermo Fisher R37606
Other in vitro reconstituted poly-nucleosome on magnetic beads This work EMD-42599
Other in vitro reconstituted H1-GFP bound nucleosome (MagIC-cryo-EM) This work EMD-42598
Other Xenopus egg extract H1-GFP bound nucleosome structure containing both interphase and metaphase particles (MagIC-cryo-EM) This work EMD-42594
Other interphase Xenopus egg extract H1-GFP bound nucleosome (MagIC-cryo-EM) This work EMD-42596
Other metaphase Xenopus egg extract H1-GFP bound nucleosome (MagIC-cryo-EM) This work EMD-42597
Other Averaged NPM2-H1.8-GFP structure (MagIC-cryo-EM) This work EMD-43238
Other open NPM2-H1.8-GFP structure (MagIC-cryo-EM) This work EMD-43239
Other closed NPM2-H1.8-GFP structure (MagIC-cryo-EM) This work EMD- 43240
Other averaged NPM2-H1.8-GFP structure This work PDB 8VHI
Other open NPM2-H1.8-GFP structure This work PDB 8VHJ
Other closed NPM2-H1.8-GFP structure This work PDB 8VHK
Recombinant DNA reagent pET21-SPY-His6-tag streptavidin This work Addgene 214836
Recombinant DNA reagent pET21-streptavidin This work Addgene 214835
Recombinant DNA reagent pQE80-His14-bdSUMO-Cys-30nm-SAH-SPYcatcher003 This work Addgene 214839
Recombinant DNA reagent pQE80-His14-bdSUMO-Cys-60 nm-SAH-SPYcatcher003 This work Addgene 214840
Recombinant DNA reagent pQE80-His14-bdSUMO-Cys-3HB-SPYcatcher003 This work Addgene 214838
Recombinant DNA reagent pQE80-SPYtag-GFP enhancer nanobody This work Addgene 214837
Recombinant DNA reagent Xenopus laevis NASCO Wild type
Recombinant DNA reagent pSF1389 Frey and Görlich, 2014 Addgene 104962
Recombinant DNA reagent pCDNA-FRT-FAK30 Ritt et al., 2013 Addgene 59121
Recombinant DNA reagent pET21a-Streptavidin-Alive Howarth et al., 2006 Addgene 20860
Software, algorithm MASCOT through Proteome Discoverer v.1.4 Thermo Scientific N/A
Software, algorithm MOTIONCOR2 Zheng et al., 2017 https://emcore.ucsf.edu/ucsf-software
Software, algorithm RELION v4 Scheres, 2012; Scheres, 2022 https://github.com/3dem/relion
Software, algorithm CryoSPARC v3 and v4 Punjani et al., 2017 https://cryosparc.com
Software, algorithm Chimera Pettersen et al., 2004 https://www.cgl.ucsf.edu/chimera/
Software, algorithm ChimaraX Pettersen et al., 2004 https://www.rbvi.ucsf.edu/chimerax/
Software, algorithm Topaz v0.2 Bepler et al., 2019a; Bepler et al., 2019b https://github.com/tbepler/topaz
Software, algorithm Bsoft Cardone et al., 2013 https://lsbr.niams.nih.gov/bsoft/
Software, algorithm Coot Emsley and Cowtan, 2004 https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/
Software, algorithm PHENIX Liebschner et al., 2019 https://phenix-online.org/documentation/reference/refinement.html
Software, algorithm APBS Baker et al., 2001 https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/apbs/apbs.html
Software, algorithm PDB2PQR Dolinsky et al., 2007 https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html
Software, algorithm SWISS-MODEL Waterhouse et al., 2018 https://swissmodel.expasy.org
Software, algorithm RING 2.0 webserver Piovesan et al., 2016 http://old.protein.bio.unipd.it/ring/
Software, algorithm Pyem v0.5 Asarnow et al., 2019 https://github.com/asarnow/pyem
Software, algorithm ImageJ Schneider et al., 2012 RRID:SCR_003070, https://imagej.nih.gov/ij/
Software, algorithm Python Python Software Foundation https://www.python.org
Software, algorithm Jupyter Notebook Project Jupyter https://jupyter.org
Software, algorithm Microsoft Excel Microsoft https://www.microsoft.com/en-us/microsoft-365/excel
Software, algorithm Soft-WoRx (Applied Precision) SoftWoRx software RRID:SCR_019157
Software, algorithm Fiji (ver. 2.9.0) Schindelin et al., 2012 RRID:SCR_002285, https://imagej.net/software/fiji/downloads
Software, algorithm RStudio ver. RSTUDIO-2023.09.1–494 RStudio Team, 2020 https://posit.co/download/rstudio-desktop/
Software, algorithm R (ver. 4.2.2) R Development Core Team, 2021 https://www.R-project.org/
Software, algorithm ggplot2 Wickham et al., 2016 https://ggplot2.tidyverse.org/
Software, algorithm ggthemes (v5.1.0.9000) Arnold, 2024 https://jrnold.github.io/ggthemes/
Software, algorithm ggpubr Kassambara, 2023 https://rpkgs.datanovia.com/ggpubr/
Software, algorithm dplyr Wickham et al., 2023 https://dplyr.tidyverse.org/
Software, algorithm lawstat Hui et al., 2008 https://doi.org/10.18637/jss.v028.i03
Software, algorithm see Lüdecke et al., 2021 https://joss.theoj.org/papers/10.21105/joss.03393
Software, algorithm scales Wickham et al., 2025 https://scales.r-lib.org
Software, algorithm GIMP software (ver. 4.2.2). GIMP (GNU Image Manipulation Program) https://gimp.org
Software, algorithm Inkscape 1.2 Inkscape Developers 2022 https://inkscape.org/
Software, algorithm ColabFold v1.5.5 Mirdita et al., 2022; Mirdita et al., 2025 https://github.com/sokrypton/ColabFold
Software, algorithm Starmap v1.2.15 Lugmayr et al., 2023a; Lugmayr et al., 2023b https://github.com/wlugmayr/chimerax-starmap
Other Xenopus laevis MS database Wühr et al., 2014 https://scholar.princeton.edu/wuehr/protein-concentrations-xenopus-egg
Other Centrifuge rotor Beckman Coulter SX241.5
Other Ultra centrifuge rotor Beckman Coulter SW55Ti
Other Ultra centrifuge rotor Beckman Coulter SW40Ti
Other Centrifuge rotor Beckman Coulter JS 5.3
Other Centrifuge Beckman Coulter Allegron X-30R
Other Ultra centrifuge Beckman Coulter Optima L80
Other Centrifuge Beckman Coulter Avanti J-26S
Other Imaging System Li-Cor Odyssey Infrared Imaging System
Other LC-MS/MS system Thermo Scientific Dionex3000 HPLC, NCS3500RS nano- and microflow pump, Q-Exactive HF mass spectrometer
Other Plunge freezer FEI Vitrobot Mark IV
Other Plasma Cleaner Gatan Solarus II
Other Cryo-EM FEI Talos Arctica TEM
Other Cryo-EM FEI Titan Krios TEM
Other Cryo-EM detector GATAN K2 Camera
Other Cryo-EM detector GATAN K3 Camera
Other N52 neodymium magnets DIYMAG D40x20–2P-NEW
Other Cryo-EM grid Quantifoil Gold R 1.2/1.3 300
Other Spectrophotometers Thermo Scientific Nanodrop ND-2000C
Other Centrifuge rotor Beckman Coulter JS 7.5
Other Fluorescence microscope Applied Precision DeltaVision Image Restoration microscope