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- PDB-28oe: Human PRC1.4 in complex with native UBCH5C bound to a H3Kc27me3 m... -

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Basic information

Entry
Database: PDB / ID: 28oe
TitleHuman PRC1.4 in complex with native UBCH5C bound to a H3Kc27me3 mononucleosome
Components
  • (DNA (151-MER)) x 2
  • Chromobox 7
  • E3 ubiquitin-protein ligase RING2
  • Histone H2A
  • Histone H2B
  • Histone H3
  • Histone H4
  • Isoform 2 of Polyhomeotic-like protein 2
  • Polycomb complex protein BMI-1
  • Ubiquitin-conjugating enzyme E2 D3
KeywordsGENE REGULATION / PRC1 / PRC1.4 / nucleosome / UBCH5C / H3Kc27me3
Function / homology
Function and homology information


histone H2AK119 ubiquitin ligase activity / segment specification / RING-like zinc finger domain binding / ubiquitin-protein transferase activator activity / positive regulation of immature T cell proliferation in thymus / sex chromatin / germ cell development / PcG protein complex / PRC1 complex / (E3-independent) E2 ubiquitin-conjugating enzyme ...histone H2AK119 ubiquitin ligase activity / segment specification / RING-like zinc finger domain binding / ubiquitin-protein transferase activator activity / positive regulation of immature T cell proliferation in thymus / sex chromatin / germ cell development / PcG protein complex / PRC1 complex / (E3-independent) E2 ubiquitin-conjugating enzyme / SUMOylation of DNA methylation proteins / SUMOylation of RNA binding proteins / protein K11-linked ubiquitination / protein K6-linked ubiquitination / positive regulation of ubiquitin-protein transferase activity / E2 ubiquitin-conjugating enzyme / negative regulation of gene expression, epigenetic / hemopoiesis / Transcriptional Regulation by E2F6 / Differentiation of naive CD4+ T cells to T helper 2 cells (Th2 cells) / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / ubiquitin conjugating enzyme activity / MLL1 complex / positive regulation of B cell proliferation / SUMOylation of DNA damage response and repair proteins / ubiquitin ligase complex / heterochromatin / protein K48-linked ubiquitination / SUMOylation of transcription cofactors / positive regulation of fibroblast proliferation / Regulation of PTEN gene transcription / SUMOylation of chromatin organization proteins / promoter-specific chromatin binding / epigenetic regulation of gene expression / euchromatin / RING-type E3 ubiquitin transferase / nucleosomal DNA binding / protein polyubiquitination / ubiquitin-protein transferase activity / regulation of gene expression / structural constituent of chromatin / ubiquitin protein ligase activity / nucleosome / nucleosome assembly / heterochromatin formation / histone binding / Oxidative Stress Induced Senescence / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear body / protein ubiquitination / endosome membrane / chromosome / chromatin remodeling / ribonucleoprotein complex / protein heterodimerization activity / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / zinc ion binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Unstructured region on Polyhomeotic-like protein 1 and 2 / Zinc finger, FCS-type / FCS-type zinc finger superfamily / Chromobox protein homolog 7 / Zinc finger, FCS-type / Zinc finger FCS-type profile. / CBX family C-terminal motif / CBX family C-terminal motif / E3 ubiquitin-protein ligase RING2 / E3 ubiquitin-protein ligase RING1/RING2 ...Unstructured region on Polyhomeotic-like protein 1 and 2 / Zinc finger, FCS-type / FCS-type zinc finger superfamily / Chromobox protein homolog 7 / Zinc finger, FCS-type / Zinc finger FCS-type profile. / CBX family C-terminal motif / CBX family C-terminal motif / E3 ubiquitin-protein ligase RING2 / E3 ubiquitin-protein ligase RING1/RING2 / RAWUL domain / RAWUL domain RING finger- and WD40-associated ubiquitin-like / : / Chromo domain subgroup / linker histone H1 and H5 family / Linker histone H1/H5, domain H15 / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 / Zinc finger, C3HC4 type (RING finger) / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / SAM domain (Sterile alpha motif) / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / SAM domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / : / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Zinc finger RING-type profile. / Zinc finger, RING-type / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H2B / Histone H3 / Chromobox 7 / Polycomb complex protein BMI-1 / Histone H4 / Ubiquitin-conjugating enzyme E2 D3 / Histone H2A ...DNA / DNA (> 10) / DNA (> 100) / Histone H2B / Histone H3 / Chromobox 7 / Polycomb complex protein BMI-1 / Histone H4 / Ubiquitin-conjugating enzyme E2 D3 / Histone H2A / Polyhomeotic-like protein 2 / E3 ubiquitin-protein ligase RING2
Similarity search - Component
Biological speciesHomo sapiens (human)
Xenopus (frog)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.74 Å
AuthorsCiapponi, M. / Mueller, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nat Struct Mol Biol / Year: 2026
Title: Cryo-EM structure, enzymatic activity and genome targeting of canonical PRC1.
Authors: Maria Ciapponi / Martina Cafiso / Sven Schkölziger / Christian Benda / Jacques Bonnet / Jürg Müller /
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 ...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.
History
DepositionFeb 10, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 16, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update
Revision 1.1Sep 23, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 2 of Polyhomeotic-like protein 2
B: Chromobox 7
C: E3 ubiquitin-protein ligase RING2
D: Polycomb complex protein BMI-1
E: Ubiquitin-conjugating enzyme E2 D3
F: Histone H3
G: Histone H4
H: Histone H2A
I: Histone H2B
J: Histone H3
K: Histone H4
L: Histone H2A
M: Histone H2B
N: DNA (151-MER)
O: DNA (151-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)408,77419
Polymers408,51215
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 9 types, 13 molecules ABCDEFJGKHLIM

#1: Protein Isoform 2 of Polyhomeotic-like protein 2 / hPH2 / Early development regulatory protein 2


Mass: 36200.988 Da / Num. of mol.: 1 / Mutation: L307E; L311E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHC2, EDR2, PH2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8IXK0
#2: Protein Chromobox 7


Mass: 18268.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBX7 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: B0QYP2
#3: Protein E3 ubiquitin-protein ligase RING2 / Huntingtin-interacting protein 2-interacting protein 3 / HIP2-interacting protein 3 / Protein DinG ...Huntingtin-interacting protein 2-interacting protein 3 / HIP2-interacting protein 3 / Protein DinG / RING finger protein 1B / RING1b / RING finger protein 2 / RING finger protein BAP-1 / RING-type E3 ubiquitin transferase RING2


Mass: 38062.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF2, BAP1, DING, HIPI3, RING1B / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q99496, RING-type E3 ubiquitin transferase
#4: Protein Polycomb complex protein BMI-1 / Polycomb group RING finger protein 4 / RING finger protein 51


Mass: 38024.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMI1, PCGF4, RNF51 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P35226
#5: Protein Ubiquitin-conjugating enzyme E2 D3 / (E3-independent) E2 ubiquitin-conjugating enzyme D3 / E2 ubiquitin-conjugating enzyme D3 / ...(E3-independent) E2 ubiquitin-conjugating enzyme D3 / E2 ubiquitin-conjugating enzyme D3 / Ubiquitin carrier protein D3 / Ubiquitin-protein ligase D3


Mass: 16706.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D3, QccE-12288 / Production host: Escherichia coli (E. coli)
References: UniProt: Q4R5N4, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme
#6: Protein Histone H3


Mass: 15271.863 Da / Num. of mol.: 2 / Mutation: C110A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus (frog) / Gene: LOC121398065, LOC108703785, LOC121398067 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A310TTQ1
#7: Protein Histone H4


Mass: 11263.231 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus (frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62798
#8: Protein Histone H2A


Mass: 13978.241 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus (frog) / Gene: LOC494591, h2ac14.L, hist1h2aj, hist1h2aj.L / Production host: Escherichia coli (E. coli) / References: UniProt: Q6AZJ8
#9: Protein Histone H2B


Mass: 13524.752 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus (frog) / Gene: XENTR_v90029538mg / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1B8Y854

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DNA chain , 2 types, 2 molecules NO

#10: DNA chain DNA (151-MER)


Mass: 76456.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#11: DNA chain DNA (151-MER)


Mass: 76716.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 1 types, 4 molecules

#12: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human PRC1.4 in complex with native UBCH5C bound to a H3Kc27me3 mononucleosome
Type: COMPLEX / Entity ID: #1-#11 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 60.45 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
12cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 304443 / Symmetry type: POINT
Atomic model building
IDPDB-ID 3D fitting-IDSource nameTypeAccession code
11AlphaFoldin silico model
24R8P

4r8p

1PDBexperimental model4R8P
RefinementHighest resolution: 2.74 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00418581
ELECTRON MICROSCOPYf_angle_d0.58226409
ELECTRON MICROSCOPYf_dihedral_angle_d27.1014891
ELECTRON MICROSCOPYf_chiral_restr0.042994
ELECTRON MICROSCOPYf_plane_restr0.0052303

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