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 28OE | pdb_000028oe

Human PRC1.4 in complex with native UBCH5C bound to a H3Kc27me3 mononucleosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.74 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history. 

Literature

Cryo-EM structure, enzymatic activity and genome targeting of canonical PRC1.

Ciapponi, M., Cafiso, M., Schkolziger, S., Benda, C., Bonnet, J., Muller, J.

(2026) Nat Struct Mol Biol 33: 1516-1526

  • DOI: https://doi.org/10.1038/s41594-026-01885-6
  • Primary Citation Related Structures: 
    28OE

  • PubMed Abstract: 

    Canonical Polycomb repressive complex 1 (cPRC1) preserves cell fate decisions by repressing aberrant transcription of developmental regulator genes. We report the cryo-electron microscopy structure of the human cPRC1 holocomplex assembled from RING1B, BMI1, PHC2 and CBX7 bound to an H3K27me3-modified mononucleosome together with the ubiquitin-conjugating enzyme UBCH5C. cPRC1 adopts a compact, highly integrated architecture in which the subunits RING1B, BMI1 and PHC2 form an extended interface that positions UBCH5C on the nucleosome to enable efficient monoubiquitination of histone H2A at K119. This organization is conserved in Drosophila, where mutational analyses identify the PHC2 ortholog Polyhomeotic (Ph) as a central scaffold and targeting factor. The Ph HD domain is required for complex assembly, whereas the Ph SAM domain is dispensable for assembly but essential for cPRC1 recruitment to Polycomb target genes and productive H2A monoubiquitination at these loci.


  • Organizational Affiliation: 
    • Laboratory of Chromatin Biology, Max-Planck Institute of Biochemistry, Martinsried, Germany.

Macromolecule Content 

  • Total Structure Weight: 408.77 kDa 
  • Atom Count: 17,632 
  • Modeled Residue Count: 1,730 
  • Deposited Residue Count: 2,784 
  • Unique protein chains: 9
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Isoform 2 of Polyhomeotic-like protein 2327Homo sapiensMutation(s): 2 
Gene Names: PHC2, EDR2, PH2
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IXK0 (Homo sapiens)
Explore Q8IXK0 
Go to UniProtKB:  Q8IXK0
PHAROS:  Q8IXK0
GTEx:  ENSG00000134686 
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UniProt GroupQ8IXK0
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Chromobox 7162Homo sapiensMutation(s): 0 
Gene Names: CBX7
UniProt & NIH Common Fund Data Resources
Find proteins for B0QYP2 (Homo sapiens)
Explore B0QYP2 
Go to UniProtKB:  B0QYP2
GTEx:  ENSG00000100307 
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UniProt GroupB0QYP2
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RING2340Homo sapiensMutation(s): 0 
Gene Names: RNF2, BAP1, DING, HIPI3, RING1B
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q99496 (Homo sapiens)
Explore Q99496 
Go to UniProtKB:  Q99496
PHAROS:  Q99496
GTEx:  ENSG00000121481 
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UniProt GroupQ99496
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Polycomb complex protein BMI-1336Homo sapiensMutation(s): 0 
Gene Names: BMI1, PCGF4, RNF51
UniProt & NIH Common Fund Data Resources
Find proteins for P35226 (Homo sapiens)
Explore P35226 
Go to UniProtKB:  P35226
PHAROS:  P35226
GTEx:  ENSG00000168283 
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UniProt GroupP35226
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 D3147Homo sapiensMutation(s): 0 
Gene Names: UBE2D3, QccE-12288
EC: 2.3.2.23 (PDB Primary Data), 2.3.2.24 (PDB Primary Data)
UniProt
Find proteins for Q4R5N4 (Macaca fascicularis)
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H3
F, J
135XenopusMutation(s): 1 
Gene Names: LOC121398065, LOC108703785, LOC121398067
UniProt
Find proteins for A0A310TTQ1 (Xenopus laevis)
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H4
G, K
102XenopusMutation(s): 0 
UniProt
Find proteins for P62798 (Xenopus borealis)
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H2A
H, L
129XenopusMutation(s): 0 
Gene Names: LOC494591, h2ac14.L, hist1h2aj, hist1h2aj.L
UniProt
Find proteins for Q6AZJ8 (Xenopus laevis)
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H2B
I, M
122XenopusMutation(s): 0 
Gene Names: XENTR_v90029538mg
UniProt
Find proteins for A0A1B8Y854 (Xenopus tropicalis)
Explore A0A1B8Y854 
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UniProt GroupA0A1B8Y854
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 10
MoleculeChains LengthOrganismImage
DNA (151-MER)248Homo sapiens
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 11
MoleculeChains LengthOrganismImage
DNA (151-MER)248Homo sapiens
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.74 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2026-09-16
    Type: Initial release
  • Version 1.1: 2026-09-23
    Changes: Data collection, Database references
  • Version 1.2: 2026-10-28
    Changes: Data collection, Database references