28OE | pdb_000028oe

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

PDB DOI: https://doi.org/10.2210/pdb28OE/pdb
EM Map EMD-56669: EMDB EMDataResource

Classification: GENE REGULATION
Organism(s): Homo sapiens, Xenopus
Expression System: Trichoplusia ni, Escherichia coli
Mutation(s): Yes

Deposited: 2026-02-10 Released: 2026-09-16
Deposition Author(s): Ciapponi, M., Mueller, J.
Funding Organization(s): German Research Foundation (DFG)

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

This is version 1.0 of the entry. See complete history.

Literature

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

Ciapponi, M., Cafiso, M., Schkoelziger, S., Benda, C., Bonnet, J., Mueller, J.

(2026) Nat Struct Mol Biol

DOI: https://doi.org/10.1038/s41594-026-01885-6

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

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of Polyhomeotic-like protein 2	A	327	Homo sapiens	Mutation(s): 2 Gene Names: PHC2, EDR2, PH2
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IXK0 (Homo sapiens) Go to UniProtKB: Q8IXK0
PHAROS: Q8IXK0 GTEx: ENSG00000134686
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8IXK0-2
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromobox 7	B	162	Homo sapiens	Mutation(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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B0QYP2
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase RING2	C	340	Homo sapiens	Mutation(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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q99496
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Polycomb complex protein BMI-1	D	336	Homo sapiens	Mutation(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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P35226
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 D3	E	147	Homo sapiens	Mutation(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) Explore Q4R5N4 Go to UniProtKB: Q4R5N4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4R5N4
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3	F, J	135	Xenopus	Mutation(s): 1 Gene Names: LOC121398065, LOC108703785, LOC121398067
UniProt
Find proteins for A0A310TTQ1 (Xenopus laevis) Explore A0A310TTQ1 Go to UniProtKB: A0A310TTQ1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A310TTQ1
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	G, K	102	Xenopus	Mutation(s): 0
UniProt
Find proteins for P62798 (Xenopus borealis) Explore P62798 Go to UniProtKB: P62798
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62798
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A	H, L	129	Xenopus	Mutation(s): 0 Gene Names: LOC494591, h2ac14.L, hist1h2aj, hist1h2aj.L
UniProt
Find proteins for Q6AZJ8 (Xenopus laevis) Explore Q6AZJ8 Go to UniProtKB: Q6AZJ8
Entity Groups
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UniProt Group	Q6AZJ8
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B	I, M	122	Xenopus	Mutation(s): 0 Gene Names: XENTR_v90029538mg
UniProt
Find proteins for A0A1B8Y854 (Xenopus tropicalis) Explore A0A1B8Y854 Go to UniProtKB: A0A1B8Y854
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1B8Y854
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 10
DNA (151-MER)	N	248	Homo sapiens
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 11
DNA (151-MER)	O	248	Homo sapiens
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Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain S [auth D] SDF format, chain R [auth D] SDF format, chain Q [auth C] SDF format, chain P [auth C] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C]	P [auth C], Q [auth C], R [auth D], S [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth D]