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- EMDB-48928: Cryo-EM map of APC/C-CDC20-UBE2C-H2A/H2B crosslinked complex -

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Entry
Database: EMDB / ID: EMD-48928
TitleCryo-EM map of APC/C-CDC20-UBE2C-H2A/H2B crosslinked complex
Map dataCryo-EM map of APC/C-CDC20-UBE2C-H2A/H2B crosslinked complex
Sample
  • Complex: APC/C-CDC20-UBE2C-H2A/H2B crosslinked complex
Keywordsubiquitin ligase / histone / chromatin / ubiquitin / complex / CELL CYCLE
Function / homology
Function and homology information


metaphase/anaphase transition of cell cycle / metaphase/anaphase transition of meiosis I / Inhibition of the proteolytic activity of APC/C required for the onset of anaphase by mitotic spindle checkpoint components / mitotic checkpoint complex / positive regulation of anaphase-promoting complex-dependent catabolic process / positive regulation of exit from mitosis / regulation of meiotic nuclear division / free ubiquitin chain polymerization / positive regulation of synapse maturation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase ...metaphase/anaphase transition of cell cycle / metaphase/anaphase transition of meiosis I / Inhibition of the proteolytic activity of APC/C required for the onset of anaphase by mitotic spindle checkpoint components / mitotic checkpoint complex / positive regulation of anaphase-promoting complex-dependent catabolic process / positive regulation of exit from mitosis / regulation of meiotic nuclear division / free ubiquitin chain polymerization / positive regulation of synapse maturation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / regulation of mitotic cell cycle spindle assembly checkpoint / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / Phosphorylation of Emi1 / anaphase-promoting complex / Aberrant regulation of mitotic exit in cancer due to RB1 defects / protein branched polyubiquitination / metaphase/anaphase transition of mitotic cell cycle / regulation of meiotic cell cycle / anaphase-promoting complex-dependent catabolic process / positive regulation of synaptic plasticity / Phosphorylation of the APC/C / regulation of exit from mitosis / anaphase-promoting complex binding / (E3-independent) E2 ubiquitin-conjugating enzyme / positive regulation of mitotic metaphase/anaphase transition / positive regulation of dendrite morphogenesis / ubiquitin ligase activator activity / positive regulation of ubiquitin protein ligase activity / protein K11-linked ubiquitination / regulation of mitotic metaphase/anaphase transition / exit from mitosis / ubiquitin-ubiquitin ligase activity / mitotic sister chromatid cohesion / E2 ubiquitin-conjugating enzyme / mitotic metaphase chromosome alignment / mitotic spindle assembly checkpoint signaling / ubiquitin conjugating enzyme activity / Regulation of APC/C activators between G1/S and early anaphase / ubiquitin-like protein ligase binding / cullin family protein binding / Transcriptional Regulation by VENTX / mitotic spindle assembly / ubiquitin ligase complex / enzyme-substrate adaptor activity / positive regulation of axon extension / ubiquitin-like ligase-substrate adaptor activity / heterochromatin / protein K48-linked ubiquitination / intercellular bridge / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / Resolution of Sister Chromatid Cohesion / nuclear periphery / regulation of mitotic cell cycle / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / SCF-beta-TrCP mediated degradation of Emi1 / Assembly of the pre-replicative complex / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / RHO GTPases Activate Formins / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / brain development / kinetochore / CDK-mediated phosphorylation and removal of Cdc6 / spindle / protein polyubiquitination / spindle pole / neuron projection development / ubiquitin-protein transferase activity / mitotic spindle / Separation of Sister Chromatids / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / nervous system development / mitotic cell cycle / microtubule cytoskeleton / Senescence-Associated Secretory Phenotype (SASP) / ubiquitin-dependent protein catabolic process / protein phosphatase binding / molecular adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / cell differentiation / Ub-specific processing proteases / protein ubiquitination / cell division / negative regulation of gene expression / intracellular membrane-bounded organelle / centrosome / ubiquitin protein ligase binding / nucleolus / zinc ion binding / nucleoplasm / ATP binding / nucleus / plasma membrane
Similarity search - Function
Anaphase-promoting complex subunit 15 / Anaphase-promoting complex subunit 15 / : / CDC20/Fizzy WD40 domain / The WD repeat Cdc20/Fizzy family / : / APC4, WD40 domain C-terminal half / Anaphase-promoting complex subunit 4, metazoa / Anaphase-promoting complex subunit 1, C-terminal / Anaphase-promoting complex subunit 1, middle domain ...Anaphase-promoting complex subunit 15 / Anaphase-promoting complex subunit 15 / : / CDC20/Fizzy WD40 domain / The WD repeat Cdc20/Fizzy family / : / APC4, WD40 domain C-terminal half / Anaphase-promoting complex subunit 4, metazoa / Anaphase-promoting complex subunit 1, C-terminal / Anaphase-promoting complex subunit 1, middle domain / : / : / : / Anaphase-promoting complex subunit 1 WD40 beta-propeller domain / Anaphase-promoting complex sub unit 1 C-terminal domain / Anaphase-promoting complex subunit 1 middle domain / APC1 beta sandwich domain / Anaphase-promoting complex subunit 5, N-terminal domain / Anaphase-promoting complex subunit 16 / Anaphase-promoting complex, subunit 16 / Cdc23 / Apc13 / Anaphase promoting complex subunit 8 / Cdc23 / Apc13p protein / Anaphase-promoting complex subunit 4 / Anaphase-promoting complex subunit 4 long domain / Anaphase-promoting complex subunit 1 / Anaphase-promoting complex subunit 5 domain / Anaphase-promoting complex subunit 5 / Anaphase-promoting complex subunit 5 / Anaphase-promoting complex, cyclosome, subunit 4 / Anaphase-promoting complex subunit APC10/Doc1 / Anaphase-promoting complex, subunit CDC26 / Anaphase-promoting complex APC subunit CDC26 / Anaphase-promoting complex subunit 11, RING-H2 finger / Anaphase-promoting complex subunit 11 RING-H2 finger / Anaphase-promoting complex subunit 2, C-terminal / Anaphase-promoting complex subunit 2 / Anaphase promoting complex (APC) subunit 2 / Anaphase promoting complex (APC) subunit 2 / APC10/DOC domain / Anaphase-promoting complex, subunit 10 (APC10) / DOC domain profile. / Anaphase-promoting complex, subunit 10 (APC10) / Anaphase-promoting complex, cyclosome, subunit 3 / TPR repeat / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / Tetratricopeptide repeat / : / : / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / Tetratricopeptide repeat / Tetratricopeptide repeat / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Tetratricopeptide repeat / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Galactose-binding-like domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 C / Cell division cycle protein 27 homolog / Anaphase-promoting complex subunit 15 / Cell division cycle protein 20 homolog / Cell division cycle protein 16 homolog / Anaphase-promoting complex subunit CDC26 / Anaphase-promoting complex subunit 16 / Anaphase-promoting complex subunit 13 / Anaphase-promoting complex subunit 1 / Anaphase-promoting complex subunit 11 ...Ubiquitin-conjugating enzyme E2 C / Cell division cycle protein 27 homolog / Anaphase-promoting complex subunit 15 / Cell division cycle protein 20 homolog / Cell division cycle protein 16 homolog / Anaphase-promoting complex subunit CDC26 / Anaphase-promoting complex subunit 16 / Anaphase-promoting complex subunit 13 / Anaphase-promoting complex subunit 1 / Anaphase-promoting complex subunit 11 / Cell division cycle protein 23 homolog / Anaphase-promoting complex subunit 7 / Anaphase-promoting complex subunit 5 / Anaphase-promoting complex subunit 4 / Anaphase-promoting complex subunit 2 / Anaphase-promoting complex subunit 10
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsSkrajna A / Bordrug T / Brown NG / McGinty RK
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM133498 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM128855 United States
National Science Foundation (NSF, United States)DGE-1650116 United States
American Cancer Society132609-PF-18-153-01-DMC United States
CitationJournal: Nat Commun / Year: 2025
Title: APC/C-mediated ubiquitylation of extranucleosomal histone complexes lacking canonical degrons.
Authors: Aleksandra Skrajna / Tatyana Bodrug / Raquel C Martinez-Chacin / Caleb B Fisher / Kaeli A Welsh / Holly C Simmons / Eyla C Arteaga / Jake M Simmons / Mohamed A Nasr / Kyle M LaPak / Anh ...Authors: Aleksandra Skrajna / Tatyana Bodrug / Raquel C Martinez-Chacin / Caleb B Fisher / Kaeli A Welsh / Holly C Simmons / Eyla C Arteaga / Jake M Simmons / Mohamed A Nasr / Kyle M LaPak / Anh Nguyen / Mai T Huynh / Isabel Fargo / Joshua G Welfare / Yani Zhao / David S Lawrence / Dennis Goldfarb / Nicholas G Brown / Robert K McGinty /
Abstract: Non-degradative histone ubiquitylation plays a myriad of well-defined roles in the regulation of gene expression and choreographing DNA damage repair pathways. In contrast, the contributions of ...Non-degradative histone ubiquitylation plays a myriad of well-defined roles in the regulation of gene expression and choreographing DNA damage repair pathways. In contrast, the contributions of degradative histone ubiquitylation on genomic processes has remained elusive. Recently, the APC/C has been shown to ubiquitylate histones to regulate gene expression in pluripotent cells, but the molecular mechanism is unclear. Here we show that despite directly binding to the nucleosome through subunit APC3, the APC/C is unable to ubiquitylate nucleosomal histones. In contrast, extranucleosomal H2A/H2B and H3/H4 complexes are broadly ubiquitylated by the APC/C in an unexpected manner. Using a combination of cryo-electron microscopy (cryo-EM) and biophysical and enzymatic assays, we demonstrate that APC8 and histone tails direct APC/C-mediated polyubiquitylation of core histones in the absence of traditional APC/C substrate degron sequences. Taken together, our work implicates APC/C-nucleosome tethering in the degradation of diverse chromatin-associated proteins and extranucleosomal histones for the regulation of transcription and the cell cycle and for preventing toxicity due to excess histone levels.
History
DepositionFeb 4, 2025-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48928.png

Downloads & links

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Map

FileDownload / File: emd_48928.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of APC/C-CDC20-UBE2C-H2A/H2B crosslinked complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.91 Å/pix.
x 480 pix.
= 436.8 Å		0.91 Å/pix.
x 480 pix.
= 436.8 Å		0.91 Å/pix.
x 480 pix.
= 436.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.91 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0026
Minimum - Maximum-0.008600567 - 0.019821595
Average (Standard dev.)-0.0000039399847 (±0.0006437156)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 436.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Cryo-EM half map 2 of APC/C-CDC20-UBE2C-H2A/H2B crosslinked complex

Fileemd_48928_half_map_1.map
AnnotationCryo-EM half map 2 of APC/C-CDC20-UBE2C-H2A/H2B crosslinked complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM half map 1 of APC/C-CDC20-UBE2C-H2A/H2B crosslinked complex

Fileemd_48928_half_map_2.map
AnnotationCryo-EM half map 1 of APC/C-CDC20-UBE2C-H2A/H2B crosslinked complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : APC/C-CDC20-UBE2C-H2A/H2B crosslinked complex

EntireName: APC/C-CDC20-UBE2C-H2A/H2B crosslinked complex
Components
  • Complex: APC/C-CDC20-UBE2C-H2A/H2B crosslinked complex

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Supramolecule #1: APC/C-CDC20-UBE2C-H2A/H2B crosslinked complex

SupramoleculeName: APC/C-CDC20-UBE2C-H2A/H2B crosslinked complex / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.2 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE
DetailsThis sample was mono disperse.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8tau

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 183499
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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