9N9S | pdb_00009n9s

Model of APC/C-CDC20-UBE2C from H3/H4-bound complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

APC/C-mediated ubiquitylation of extranucleosomal histone complexes lacking canonical degrons.

Skrajna, A.Bodrug, T.Martinez-Chacin, R.C.Fisher, C.B.Welsh, K.A.Simmons, H.C.Arteaga, E.C.Simmons, J.M.Nasr, M.A.LaPak, K.M.Nguyen, A.Huynh, M.T.Fargo, I.Welfare, J.G.Zhao, Y.Lawrence, D.S.Goldfarb, D.Brown, N.G.McGinty, R.K.

(2025) Nat Commun 16: 2561-2561

  • DOI: https://doi.org/10.1038/s41467-025-57384-7
  • Primary Citation of Related Structures:  
    9N9R, 9N9S

  • PubMed 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 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.


  • Organizational Affiliation
    • Division of Chemical Biology and Medicinal Chemistry and Center for Integrated Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Anaphase-promoting complex subunit 11,944Homo sapiensMutation(s): 21 
Gene Names: ANAPC1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H1A4 (Homo sapiens)
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Go to UniProtKB:  Q9H1A4
PHAROS:  Q9H1A4
GTEx:  ENSG00000153107 
Entity Groups  
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UniProt GroupQ9H1A4
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Anaphase-promoting complex subunit 11B [auth C]84Homo sapiensMutation(s): 0 
Gene Names: ANAPC11HSPC214
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Find proteins for Q9NYG5 (Homo sapiens)
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PHAROS:  Q9NYG5
GTEx:  ENSG00000141552 
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UniProt GroupQ9NYG5
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Anaphase-promoting complex subunit 15C [auth D]56Homo sapiensMutation(s): 0 
Gene Names: ANAPC15
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Find proteins for P60006 (Homo sapiens)
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PHAROS:  P60006
GTEx:  ENSG00000110200 
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UniProt GroupP60006
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Anaphase-promoting complex subunit CDC26D [auth G],
S [auth W]
85Homo sapiensMutation(s): 3 
Gene Names: CDC26ANAPC12C9orf17
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Find proteins for Q8NHZ8 (Homo sapiens)
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PHAROS:  Q8NHZ8
GTEx:  ENSG00000176386 
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UniProt GroupQ8NHZ8
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Anaphase-promoting complex subunit 16E [auth H]58Homo sapiensMutation(s): 0 
Gene Names: ANAPC16C10orf104CENP-27
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Find proteins for Q96DE5 (Homo sapiens)
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PHAROS:  Q96DE5
GTEx:  ENSG00000166295 
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UniProt GroupQ96DE5
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Anaphase-promoting complex subunit 4F [auth I]808Homo sapiensMutation(s): 2 
Gene Names: ANAPC4APC4
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Find proteins for Q9UJX5 (Homo sapiens)
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PHAROS:  Q9UJX5
GTEx:  ENSG00000053900 
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UniProt GroupQ9UJX5
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division cycle protein 27 homologG [auth J],
M [auth P]
824Homo sapiensMutation(s): 14 
Gene Names: CDC27ANAPC3D0S1430ED17S978E
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Find proteins for P30260 (Homo sapiens)
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PHAROS:  P30260
GTEx:  ENSG00000004897 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division cycle protein 16 homologH [auth K],
P [auth S]
620Homo sapiensMutation(s): 5 
Gene Names: CDC16ANAPC6
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Find proteins for Q13042 (Homo sapiens)
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PHAROS:  Q13042
GTEx:  ENSG00000130177 
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UniProt GroupQ13042
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Anaphase-promoting complex subunit 10I [auth L]185Homo sapiensMutation(s): 1 
Gene Names: ANAPC10APC10
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Find proteins for Q9UM13 (Homo sapiens)
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PHAROS:  Q9UM13
GTEx:  ENSG00000164162 
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UniProt GroupQ9UM13
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Anaphase-promoting complex subunit 13J [auth M]74Homo sapiensMutation(s): 0 
Gene Names: ANAPC13
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Find proteins for Q9BS18 (Homo sapiens)
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PHAROS:  Q9BS18
GTEx:  ENSG00000129055 
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UniProt GroupQ9BS18
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Anaphase-promoting complex subunit 2K [auth N]720Homo sapiensMutation(s): 0 
Gene Names: ANAPC2APC2KIAA1406
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Find proteins for Q9UJX6 (Homo sapiens)
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PHAROS:  Q9UJX6
GTEx:  ENSG00000176248 
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UniProt GroupQ9UJX6
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Anaphase-promoting complex subunit 5L [auth O]755Homo sapiensMutation(s): 7 
Gene Names: ANAPC5APC5
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Find proteins for Q9UJX4 (Homo sapiens)
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PHAROS:  Q9UJX4
GTEx:  ENSG00000089053 
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UniProt GroupQ9UJX4
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 CN [auth Q]145Homo sapiensMutation(s): 0 
Gene Names: UBE2C
EC: 2.3.2.24 (UniProt), 2.3.2.23 (UniProt)
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Find proteins for O00762 (Homo sapiens)
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PHAROS:  O00762
GTEx:  ENSG00000175063 
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UniProt GroupO00762
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division cycle protein 20 homologO [auth R]499Homo sapiensMutation(s): 0 
Gene Names: CDC20
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Find proteins for Q12834 (Homo sapiens)
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PHAROS:  Q12834
GTEx:  ENSG00000117399 
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UniProt GroupQ12834
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division cycle protein 23 homologQ [auth U],
R [auth V]
597Homo sapiensMutation(s): 5 
Gene Names: CDC23ANAPC8
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Find proteins for Q9UJX2 (Homo sapiens)
Explore Q9UJX2 
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PHAROS:  Q9UJX2
GTEx:  ENSG00000094880 
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UniProt GroupQ9UJX2
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Anaphase-promoting complex subunit 7T [auth Y],
U [auth Z]
565Homo sapiensMutation(s): 0 
Gene Names: ANAPC7APC7
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Find proteins for Q9UJX3 (Homo sapiens)
Explore Q9UJX3 
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PHAROS:  Q9UJX3
GTEx:  ENSG00000196510 
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UniProt GroupQ9UJX3
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM133498
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM128855
National Science Foundation (NSF, United States)United StatesDGE-1650116
American Cancer SocietyUnited States132609-PF-18-153-01-DMC

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-16
    Type: Initial release