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- EMDB-64872: Cryo-EM structure of the cPRC1-di-nucleosome (tight) complex -

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Basic information

Entry
Database: EMDB / ID: EMD-64872
TitleCryo-EM structure of the cPRC1-di-nucleosome (tight) complex
Map dataComposite EM map of the cPRC1-di-nucleosome(loose) complex
Sample
  • Complex: cPRC1-di-nucleosome(tight) complex
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-H
    • Protein or peptide: Histone H2B type 1-C/E/F/G/I
    • DNA: DNA (276-MER)
    • DNA: DNA (276-MER)
    • Protein or peptide: Polycomb complex protein BMI-1
    • Protein or peptide: E3 ubiquitin-protein ligase RING2
  • Ligand: ZINC ION
Keywordsnucleosome modification / transcriptional regulation / GENE REGULATION
Function / homology
Function and homology information


histone H2AK119 ubiquitin ligase activity / PRC1 complex / regulation of kidney development / RING-like zinc finger domain binding / segment specification / rostrocaudal neural tube patterning / ubiquitin-protein transferase activator activity / regulation of adaxial/abaxial pattern formation / somatic stem cell division / embryonic skeletal system morphogenesis ...histone H2AK119 ubiquitin ligase activity / PRC1 complex / regulation of kidney development / RING-like zinc finger domain binding / segment specification / rostrocaudal neural tube patterning / ubiquitin-protein transferase activator activity / regulation of adaxial/abaxial pattern formation / somatic stem cell division / embryonic skeletal system morphogenesis / sex chromatin / positive regulation of immature T cell proliferation in thymus / PcG protein complex / SUMOylation of DNA methylation proteins / gastrulation with mouth forming second / SUMOylation of RNA binding proteins / anterior/posterior axis specification / positive regulation of ubiquitin-protein transferase activity / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of gene expression, epigenetic / Transcriptional Regulation by E2F6 / germ cell development / humoral immune response / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / MLL1 complex / hemopoiesis / negative regulation of apoptotic signaling pathway / : / cellular response to interleukin-1 / cellular response to dexamethasone stimulus / ubiquitin ligase complex / SUMOylation of DNA damage response and repair proteins / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / positive regulation of B cell proliferation / Replacement of protamines by nucleosomes in the male pronucleus / heterochromatin / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / SUMOylation of transcription cofactors / Deposition of new CENPA-containing nucleosomes at the centromere / epigenetic regulation of gene expression / telomere organization / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / Assembly of the ORC complex at the origin of replication / Meiotic synapsis / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / SUMOylation of chromatin organization proteins / Regulation of PTEN gene transcription / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / innate immune response in mucosa / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / promoter-specific chromatin binding / apoptotic signaling pathway / Transcriptional regulation by small RNAs / euchromatin / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / brain development / G2/M DNA damage checkpoint / Negative Regulation of CDH1 Gene Transcription / NoRC negatively regulates rRNA expression / RING-type E3 ubiquitin transferase / PKMTs methylate histone lysines / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / positive regulation of fibroblast proliferation / Transcriptional regulation of granulopoiesis / RMTs methylate histone arginines / Metalloprotease DUBs / HCMV Early Events / structural constituent of chromatin / ubiquitin protein ligase activity / UCH proteinases / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / mitotic cell cycle
Similarity search - Function
E3 ubiquitin-protein ligase RING2 / E3 ubiquitin-protein ligase RING1/RING2 / RAWUL domain / RAWUL domain RING finger- and WD40-associated ubiquitin-like / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / : / Histone H2A conserved site ...E3 ubiquitin-protein ligase RING2 / E3 ubiquitin-protein ligase RING1/RING2 / RAWUL domain / RAWUL domain RING finger- and WD40-associated ubiquitin-like / Zinc finger, C3HC4 type (RING finger) / 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
Similarity search - Domain/homology
Polycomb complex protein BMI-1 / Histone H4 / Histone H2B type 1-C/E/F/G/I / Histone H3.1 / Histone H2A type 1-H / E3 ubiquitin-protein ligase RING2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsYu Y / Cai D / Zhang YZ / Huang J
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural mechanisms of PRC1-mediated interplay between gene repression and activation
Authors: Yu Y / Cai D / Zhang YZ / Huang J
History
DepositionMay 30, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64872.png

Downloads & links

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Map

FileDownload / File: emd_64872.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite EM map of the cPRC1-di-nucleosome(loose) complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 240 pix.
= 264. Å		1.1 Å/pix.
x 240 pix.
= 264. Å		1.1 Å/pix.
x 240 pix.
= 264. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007
Minimum - Maximum0.0 - 0.077072
Average (Standard dev.)0.001221678 (±0.002454511)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 264.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : cPRC1-di-nucleosome(tight) complex

EntireName: cPRC1-di-nucleosome(tight) complex
Components
  • Complex: cPRC1-di-nucleosome(tight) complex
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-H
    • Protein or peptide: Histone H2B type 1-C/E/F/G/I
    • DNA: DNA (276-MER)
    • DNA: DNA (276-MER)
    • Protein or peptide: Polycomb complex protein BMI-1
    • Protein or peptide: E3 ubiquitin-protein ligase RING2
  • Ligand: ZINC ION

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Supramolecule #1: cPRC1-di-nucleosome(tight) complex

SupramoleculeName: cPRC1-di-nucleosome(tight) complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Histone H3.1

MacromoleculeName: Histone H3.1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.437167 KDa
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEACEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.1

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.394426 KDa
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A type 1-H

MacromoleculeName: Histone H2A type 1-H / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.935305 KDa
SequenceString:
MSGRGKQGGK ARAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIR NDEELNKLLG KVTIAQGGVL PNIQAVLLPK KTESHHKAK

UniProtKB: Histone H2A type 1-H

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Macromolecule #4: Histone H2B type 1-C/E/F/G/I

MacromoleculeName: Histone H2B type 1-C/E/F/G/I / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.937213 KDa
SequenceString:
MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSV YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSSK

UniProtKB: Histone H2B type 1-C/E/F/G/I

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Macromolecule #7: Polycomb complex protein BMI-1

MacromoleculeName: Polycomb complex protein BMI-1 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.006062 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHRTTRIKIT ELNPHLMCVL CGGYFIDATT IIECLHSFCK TCIVRYLETS KYCPICDVQV HKTRPLLNIR SDKTLQDIVY KLVPGLFKN EMKRRRDFYA AHPSADAANG SNEDRGEVAD EDKRIITDDE IISLSIEFFD QNRLDRKVNK DKEKSKEEVN D KRYLRCPA ...String:
MHRTTRIKIT ELNPHLMCVL CGGYFIDATT IIECLHSFCK TCIVRYLETS KYCPICDVQV HKTRPLLNIR SDKTLQDIVY KLVPGLFKN EMKRRRDFYA AHPSADAANG SNEDRGEVAD EDKRIITDDE IISLSIEFFD QNRLDRKVNK DKEKSKEEVN D KRYLRCPA AMTVMHLRKF LRSKMDIPNT FQIDVMYEEE PLKDYYTLMD IAYIYTWRRN GPLPLKYRVR PTCKRMKISH QR DGLTNAG ELESDSGSDK ANSPAGGIPS TSSCLPSPST PVQSPHPQFP HISSTMNGTS NSPSGNHQSS FANRPRKSSV NGS SATSSG

UniProtKB: Polycomb complex protein BMI-1

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Macromolecule #8: E3 ubiquitin-protein ligase RING2

MacromoleculeName: E3 ubiquitin-protein ligase RING2 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.706371 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSQAVQTNGT QPLSKTWELS LYELQRTPQE AITDGLEIVV SPRSLHSELM CPICLDMLKN TMTTKECLHR FCADCIITAL RSGNKECPT CRKKLVSKRS LRPDPNFDAL ISKIYPSRDE YEAHQERVLA RINKHNNQQA LSHSIEEGLK IQAMNRLQRG K KQQIENGS ...String:
MSQAVQTNGT QPLSKTWELS LYELQRTPQE AITDGLEIVV SPRSLHSELM CPICLDMLKN TMTTKECLHR FCADCIITAL RSGNKECPT CRKKLVSKRS LRPDPNFDAL ISKIYPSRDE YEAHQERVLA RINKHNNQQA LSHSIEEGLK IQAMNRLQRG K KQQIENGS GAEDNGDSSH CSNASTHSNQ EAGPSNKRTK TSDDSGLELD NNNAAMAIDP VMDGASEIEL VFRPHPTLME KD DSAQTRY IKTSGNATVD HLSKYLAVRL ALEELRSKGE SNQMNLDTAS EKQYTIYIAT ASGQFTVLNG SFSLELVSEK YWK VNKPME LYYAPTKEHK

UniProtKB: E3 ubiquitin-protein ligase RING2

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Macromolecule #5: DNA (276-MER)

MacromoleculeName: DNA (276-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 85.179109 KDa
SequenceString: (DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC)(DA)(DC) (DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG)(DA)(DG) (DA)(DC)(DT)(DA)(DG)(DG)(DG)(DA)(DG) (DT)(DA)(DA)(DT)(DC)(DC)(DC)(DC)(DT)(DT) (DG) (DG)(DC)(DG)(DG)(DT)(DT) ...String:
(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC)(DA)(DC) (DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG)(DA)(DG) (DA)(DC)(DT)(DA)(DG)(DG)(DG)(DA)(DG) (DT)(DA)(DA)(DT)(DC)(DC)(DC)(DC)(DT)(DT) (DG) (DG)(DC)(DG)(DG)(DT)(DT)(DA)(DA) (DA)(DA)(DC)(DG)(DC)(DG)(DG)(DG)(DG)(DG) (DA)(DC) (DA)(DG)(DC)(DG)(DC)(DG)(DT) (DA)(DC)(DG)(DT)(DG)(DC)(DG)(DT)(DT)(DT) (DA)(DA)(DG) (DC)(DG)(DG)(DT)(DG)(DC) (DT)(DA)(DG)(DA)(DG)(DC)(DT)(DG)(DT)(DC) (DT)(DA)(DC)(DG) (DA)(DC)(DC)(DA)(DA) (DT)(DT)(DG)(DA)(DG)(DC)(DG)(DG)(DC)(DC) (DT)(DC)(DG)(DG)(DC) (DA)(DC)(DC)(DG) (DG)(DG)(DA)(DT)(DT)(DC)(DT)(DC)(DC)(DG) (DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG) (DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG)(DG)(DC) (DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT) (DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG)(DA)(DC) (DA)(DG)(DC)(DT)(DC)(DT)(DA)(DG) (DC) (DA)(DC)(DC)(DG)(DC)(DT)(DT)(DA)(DA)(DA) (DC)(DG)(DC)(DA)(DC)(DG)(DT)(DA)(DC) (DG)(DC)(DG)(DC)(DT)(DG)(DT)(DC)(DC)(DC) (DC)(DC)(DG)(DC)(DG)(DT)(DT)(DT)(DT)(DA) (DA)(DC)(DC)(DG)(DC)(DC)(DA)(DA)(DG) (DG)(DG)(DG)(DA)(DT)(DT)(DA)(DC)(DT)(DC) (DC) (DC)(DT)(DA)(DG)(DT)(DC)(DT)(DC) (DC)(DA)(DG)(DG)(DC)(DA)(DC)(DG)(DT)(DG) (DT)(DC) (DA)(DG)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DC)(DA)(DT)(DC)(DC)(DG)(DA)

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Macromolecule #6: DNA (276-MER)

MacromoleculeName: DNA (276-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 85.290156 KDa
SequenceString: (DT)(DC)(DG)(DG)(DA)(DT)(DG)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC)(DA) (DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG) (DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG)(DA) (DG) (DT)(DA)(DA)(DT)(DC)(DC) ...String:
(DT)(DC)(DG)(DG)(DA)(DT)(DG)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC)(DA) (DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG) (DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG)(DA) (DG) (DT)(DA)(DA)(DT)(DC)(DC)(DC)(DC) (DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT)(DA) (DA)(DA) (DA)(DC)(DG)(DC)(DG)(DG)(DG) (DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC)(DG) (DT)(DA)(DC) (DG)(DT)(DG)(DC)(DG)(DT) (DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT)(DG) (DC)(DT)(DA)(DG) (DA)(DG)(DC)(DT)(DG) (DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC)(DA) (DA)(DT)(DT)(DG)(DA) (DG)(DC)(DG)(DG) (DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA)(DC)(DC) (DG)(DG)(DG)(DA)(DT)(DT) (DC)(DT)(DC) (DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC)(DC)(DC) (DG)(DG)(DT)(DG)(DC)(DC)(DG) (DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA)(DT) (DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA) (DG) (DA)(DC)(DA)(DG)(DC)(DT)(DC)(DT)(DA)(DG) (DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT)(DA) (DA)(DA)(DC)(DG)(DC)(DA)(DC)(DG)(DT)(DA) (DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT)(DC)(DC) (DC)(DC)(DC)(DG)(DC)(DG)(DT)(DT)(DT) (DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC)(DA)(DA) (DG) (DG)(DG)(DG)(DA)(DT)(DT)(DA)(DC) (DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT)(DC)(DT) (DC)(DC) (DA)(DG)(DG)(DC)(DA)(DC)(DG) (DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT)(DA)

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Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / Number of copies: 8 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 97701
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION

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