# Structural basis of nucleosome deubiquitination by the bidentate Calypso/Asx complex **Authors:** Chi Wang, Fahui Sun, Heyu Zhao, Nan Zhang, Jiali Guan, Yuxing Zhou, Wentong Shuai, Hui Zheng, Jun He PMC · DOI: 10.1016/j.isci.2026.114958 · iScience · 2026-02-10 ## TL;DR The study reveals how a bidentate Calypso/Asx complex interacts with and removes ubiquitin from nucleosomes, enabling processive deubiquitination along chromatin. ## Contribution The cryo-EM structure of the bidentate Calypso/Asx complex bound to a nucleosome is presented, revealing asymmetric binding and a spreading mechanism. ## Key findings - Cryo-EM shows asymmetric binding of the bidentate Calypso/Asx complex to ubiquitinated nucleosomes. - The positively charged C terminus of Calypso is crucial for chromatin engagement and spreading. - The bidentate complex enables processive deubiquitination along chromatin via alternating engagement. ## Abstract The Polycomb repressive complex 1 (PRC1) and PR-DUB constitute a canonical pair of histone-modifying enzymes that deposit and remove monoubiquitinated H2A at lysine 119 (H2AK119ub1), serving as a model of dynamic epigenetic regulation. In humans, PR-DUB, composed of BAP1 and ASXL1, functions as a monomeric complex, while the Drosophila homolog Calypso/Asx forms a bidentate dimer (Calypso2: Asx2) with an unclear chromatin engagement mechanism. Here, we present its cryo-EM structure bound to a nucleosome, revealing the molecular basis of interaction. Surprisingly, only one Calypso/Asx unit engages the nucleosome in a conformation similar to human BAP1/ASXL1, while the second remains disengaged. Structural and biochemical analysis of the positively charged Calypso C terminus suggests a “spreading” potential of the bidentate complex along chromatin, which was validated in vitro using nucleosome arrays. These findings support a model in which the bidentate Calypso/Asx complex enables processive deubiquitination along chromatin via alternating or cooperative engagement. •Cryo-EM reveals asymmetric bidentate Calypso/Asx binding to ubiquitinated nucleosome•The positively charged tail of Calypso is a key determinant of chromatin engagement•A bidentate Calypso/Asx complex enables spreading along chromatin Cryo-EM reveals asymmetric bidentate Calypso/Asx binding to ubiquitinated nucleosome The positively charged tail of Calypso is a key determinant of chromatin engagement A bidentate Calypso/Asx complex enables spreading along chromatin Natural sciences; Biological sciences; Structural biology ## Linked entities - **Genes:** PRC1 (protein regulator of cytokinesis 1) [NCBI Gene 9055], BAP1 (BRCA1 associated deubiquitinase 1) [NCBI Gene 8314], ASXL1 (ASXL transcriptional regulator 1) [NCBI Gene 171023], calypso (ubiquitin carboxyl-terminal hydrolase calypso) [NCBI Gene 663933], Asx (Additional sex combs) [NCBI Gene 36612] - **Proteins:** PRC1 (protein regulator of cytokinesis 1), BAP1 (BRCA1 associated deubiquitinase 1), ASXL1 (ASXL transcriptional regulator 1), calypso (ubiquitin carboxyl-terminal hydrolase calypso), Asx (Additional sex combs) - **Species:** Drosophila (taxon 7215) ## Full-text entities - **Genes:** RYBP (Ring and YY1 Binding Protein) [NCBI Gene 37601] {aka CG12190, Dmel\CG12190, dRYBP, drybp}, ASXL1 (ASXL transcriptional regulator 1) [NCBI Gene 171023] {aka BOPS, MDS}, Pc (Polycomb) [NCBI Gene 40358] {aka CG32443, CG7618, DmPc, Dmel\CG32443, Pc-G, PcG}, sxc (super sex combs) [NCBI Gene 35486] {aka BcDNA:GH04245, CG10392, DmOGT, Dmel\CG10392, OGT, Ogt}, His2Av (Histone H2A variant) [NCBI Gene 43229] {aka *i H2av, 5499, CG5499, Dmel\CG5499, H2A, H2A.F/Z}, Hcf (Host cell factor) [NCBI Gene 43788] {aka CG1710, Dmel\CG1710, HCF1, HCF_DROME, Hcf1, anon-WO0172774.48}, Asx (Additional sex combs) [NCBI Gene 36612] {aka CG8787, Dmel\CG8787, FBgn0261823, xen}, H2AC18 (H2A clustered histone 18) [NCBI Gene 8337] {aka H2A, H2A.2, H2A/O, H2A/q, H2AFO, H2a-615}, BAP1 (BRCA1 associated deubiquitinase 1) [NCBI Gene 8314] {aka HUCEP-13, KURIS, TPDS1, UBM2, UCHL2, UVM2}, His2A:CG33853 (histone H2A) [NCBI Gene 3772346] {aka CG33853, Dmel\CG33853}, feo (fascetto) [NCBI Gene 32015] {aka CG11207, Dmel\CG11207, EA86, Feo1, PRC1, Q54}, caly (calypso) [NCBI Gene 36794] {aka BAP1, CG8445, Calypso, Dmel\CG8445, Q7K5N4, bap1}, CG11700 (uncharacterized protein) [NCBI Gene 31564] {aka CR11700, Dmel\CG11700, ESTS:143G11T, ESTS:199A6T, Ub, Ubi-p5E5}, sub (subito) [NCBI Gene 44870] {aka CG12298, DmKlp54E, DmSub, Dmel\CG12298, Dub, KIF 20A} - **Diseases:** tumor (MESH:D009369) - **Chemicals:** HEPES (MESH:D006531), glycerol (MESH:D005990), GST (MESH:C059555), desthiobiotin (MESH:C004749), Cytiva (-), DMSO (MESH:D004121), Heparin (MESH:D006493), Tween-20 (MESH:D011136), PBS (MESH:D007854), glutaraldehyde (MESH:D005976), polystyrene (MESH:D011137), IPTG (MESH:D007544), ATP (MESH:D000255), agar (MESH:D000362), nitrogen (MESH:D009584), EDTA (MESH:D004492), NP-40 (MESH:C010615), salt (MESH:D012492), TCEP (MESH:C080938), NaCl (MESH:D012965), MgCl2 (MESH:D015636), kanamycin (MESH:D007612), HCl (MESH:D006851), SDS (MESH:D012967), DTT (MESH:D004229), 1,3-dichloroacetone (MESH:C047675), CHAPS (MESH:C028213), FuGENE (MESH:C411955), imidazole (MESH:C029899), water (MESH:D014867), ethane (MESH:D004980) - **Species:** Homo sapiens (human, species) [taxon 9606], Arabidopsis thaliana (mouse-ear cress, species) [taxon 3702], Drosophila melanogaster (fruit fly, species) [taxon 7227], Xenopus laevis (African clawed frog, species) [taxon 8355], Enterovirus (genus) [taxon 12059] - **Mutations:** G76C, M288R, N292R, L340R - **Cell lines:** E. coli — Mus musculus (Mouse), Hybridoma (CVCL_C5CR), High Five — Trichoplusia ni (Cabbage looper), Spontaneously immortalized cell line (CVCL_C190), BL21 (DE3) — Mus musculus (Mouse), Hybridoma (CVCL_B7HM), pETDuet-1 — Mus musculus (Mouse), Hybridoma (CVCL_C7RB), Sf9 — Spodoptera frugiperda (Fall armyworm), Spontaneously immortalized cell line (CVCL_0549) ## Full text _Full body text omitted from this summary view._ Fetch the complete paper as Markdown: https://tomesphere.com/paper/PMC12955571/full.md ## Figures 5 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12955571/full.md ## References 45 references — full list in the complete paper: https://tomesphere.com/paper/PMC12955571/full.md --- Source: https://tomesphere.com/paper/PMC12955571