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- EMDB-46823: ncPRC1RYBP bound to unmodified nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-46823
TitlencPRC1RYBP bound to unmodified nucleosome
Map datancPRC1RYBP bound to unmodified nucleosome
Sample
  • Complex: ncPRC1RYBP bound to unmodified nucleosome
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1
    • Protein or peptide: Histone H2B 1.1
    • DNA: DNA (187-MER)
    • DNA: DNA (187-MER)
    • Protein or peptide: Polycomb complex protein BMI-1
    • Protein or peptide: E3 ubiquitin-protein ligase RING2
  • Ligand: ZINC ION
KeywordsDNA complex protein / NUCLEAR PROTEIN-DNA complex
Function / homology
Function and homology information


regulation of adaxial/abaxial pattern formation / histone H2AK119 ubiquitin ligase activity / PRC1 complex / RING-like zinc finger domain binding / regulation of kidney development / segment specification / sex chromatin / rostrocaudal neural tube patterning / ubiquitin-protein transferase activator activity / somatic stem cell division ...regulation of adaxial/abaxial pattern formation / histone H2AK119 ubiquitin ligase activity / PRC1 complex / RING-like zinc finger domain binding / regulation of kidney development / segment specification / sex chromatin / rostrocaudal neural tube patterning / ubiquitin-protein transferase activator activity / somatic stem cell division / embryonic skeletal system morphogenesis / 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 / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Transcriptional Regulation by E2F6 / germ cell development / hemopoiesis / humoral immune response / negative regulation of apoptotic signaling pathway / MLL1 complex / cellular response to interleukin-1 / ubiquitin ligase complex / heterochromatin / SUMOylation of DNA damage response and repair proteins / positive regulation of B cell proliferation / cellular response to dexamethasone stimulus / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / epigenetic regulation of gene expression / Regulation of PTEN gene transcription / negative regulation of DNA-binding transcription factor activity / apoptotic signaling pathway / promoter-specific chromatin binding / euchromatin / brain development / RING-type E3 ubiquitin transferase / positive regulation of fibroblast proliferation / structural constituent of chromatin / ubiquitin protein ligase activity / nucleosome / heterochromatin formation / nucleosome assembly / mitotic cell cycle / regulation of gene expression / Oxidative Stress Induced Senescence / gene expression / in utero embryonic development / protein ubiquitination / nuclear body / chromatin remodeling / protein heterodimerization activity / chromatin binding / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
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 H2B signature. ...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 H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / 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 / Histone H3 signature 1. / Zinc finger RING-type profile. / Zinc finger, RING-type / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Histone H2B 1.1 / Histone H2A type 1 / Polycomb complex protein BMI-1 / Histone H4 / Histone H3.2 / E3 ubiquitin-protein ligase RING2
Similarity search - Component
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsGodinez-Lopez V / Valencia-Sanchez MI / Armache JP / Armache K-J
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM115882 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA266978 United States
The Mark Foundation United States
CitationJournal: Nature / Year: 2024
Title: Read-write mechanisms of H2A ubiquitination by Polycomb repressive complex 1.
Authors: Victoria Godínez López / Marco Igor Valencia-Sánchez / Stephen Abini-Agbomson / Jonathan F Thomas / Rachel Lee / Pablo De Ioannes / Brian A Sosa / Jean-Paul Armache / Karim-Jean Armache /
Abstract: Epigenetic inheritance of silent chromatin domains is fundamental to cellular memory during embryogenesis, but it must overcome the dilution of repressive histone modifications during DNA replication. ...Epigenetic inheritance of silent chromatin domains is fundamental to cellular memory during embryogenesis, but it must overcome the dilution of repressive histone modifications during DNA replication. One such modification, histone H2A lysine 119 monoubiquitination (H2AK119Ub), needs to be re-established by the Polycomb repressive complex 1 (PRC1) E3 ligase to restore the silent Polycomb domain. However, the exact mechanism behind this restoration remains unknown. Here, combining cryo-electron microscopy (cryo-EM) and functional approaches, we characterize the read-write mechanism of the non-canonical PRC1-containing RYBP (ncPRC1). This mechanism, which functions as a positive-feedback loop in epigenetic regulation, emphasizes the pivotal role of ncPRC1 in restoring H2AK119Ub. We observe an asymmetrical binding of ncPRC1 to H2AK119Ub nucleosomes, guided in part by the N-terminal zinc-finger domain of RYBP binding to residual H2AK119Ub on nascent chromatin. This recognition positions the RING domains of RING1B and BMI1 on the unmodified nucleosome side, enabling recruitment of the E2 enzyme to ubiquitinate H2AK119 within the same nucleosome (intra-nucleosome read-write) or across nucleosomes (inter-nucleosome read-write). Collectively, our findings provide key structural and mechanistic insights into the dynamic interplay of epigenetic regulation, highlighting the significance of ncPRC1 in H2AK119Ub restoration to sustain repressive chromatin domains.
History
DepositionSep 2, 2024-
Header (metadata) releaseNov 20, 2024-
Map releaseNov 20, 2024-
UpdateJan 15, 2025-
Current statusJan 15, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46823.png

Downloads & links

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Map

FileDownload / File: emd_46823.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationncPRC1RYBP bound to unmodified nucleosome
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 280.576 Å		1.1 Å/pix.
x 256 pix.
= 280.576 Å		1.1 Å/pix.
x 256 pix.
= 280.576 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.096 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.29
Minimum - Maximum0.0 - 1.4009088
Average (Standard dev.)0.009097605 (±0.05202739)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 280.576 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_46823_msk_1.map
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Additional map: Additional map C

Fileemd_46823_additional_1.map
AnnotationAdditional map C
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Additional map: Additional map B

Fileemd_46823_additional_2.map
AnnotationAdditional map B
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Additional map: Additional map A

Fileemd_46823_additional_3.map
AnnotationAdditional map A
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Half map: Half Map A

Fileemd_46823_half_map_1.map
AnnotationHalf Map A
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Half map: Half Map B

Fileemd_46823_half_map_2.map
AnnotationHalf Map B
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Sample components

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Entire : ncPRC1RYBP bound to unmodified nucleosome

EntireName: ncPRC1RYBP bound to unmodified nucleosome
Components
  • Complex: ncPRC1RYBP bound to unmodified nucleosome
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1
    • Protein or peptide: Histone H2B 1.1
    • DNA: DNA (187-MER)
    • DNA: DNA (187-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: ncPRC1RYBP bound to unmodified nucleosome

SupramoleculeName: ncPRC1RYBP bound to unmodified nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.435126 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEASEA YLVALFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.2

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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

MacromoleculeName: Histone H2A type 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 14.093436 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKQGGK TRAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAVR NDEELNKLLG RVTIAQGGVL PNIQSVLLPK KTESAKSAKS K

UniProtKB: Histone H2A type 1

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Macromolecule #4: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.979291 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPEPAKSAPA PKKGSKKAVT KTQKKDGKKR RKTRKESYAI YVYKVLKQVH PDTGISSKAM SIMNSFVNDV FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSAK

UniProtKB: Histone H2B 1.1

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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: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.006062 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.706371 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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 (187-MER)

MacromoleculeName: DNA (187-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 57.982918 KDa
SequenceString: (DA)(DT)(DC)(DG)(DC)(DG)(DA)(DC)(DA)(DC) (DC)(DG)(DG)(DC)(DA)(DC)(DT)(DG)(DG)(DA) (DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA) (DC) (DA)(DC)(DG)(DT)(DG)(DC) ...String:
(DA)(DT)(DC)(DG)(DC)(DG)(DA)(DC)(DA)(DC) (DC)(DG)(DG)(DC)(DA)(DC)(DT)(DG)(DG)(DA) (DA)(DC)(DA)(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)(DC)(DA)(DG)(DG)(DG)(DG)(DA)(DT) (DC)(DG)(DG)(DG)(DC)(DA)(DT)(DC) (DA) (DC)(DC)(DC)(DG)(DA)(DT)

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Macromolecule #6: DNA (187-MER)

MacromoleculeName: DNA (187-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 57.488551 KDa
SequenceString: (DA)(DT)(DC)(DG)(DG)(DG)(DT)(DG)(DA)(DT) (DG)(DC)(DC)(DC)(DG)(DA)(DT)(DC)(DC)(DC) (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT) (DC)(DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG) (DA) (DG)(DG)(DC)(DC)(DG)(DC) ...String:
(DA)(DT)(DC)(DG)(DG)(DG)(DT)(DG)(DA)(DT) (DG)(DC)(DC)(DC)(DG)(DA)(DT)(DC)(DC)(DC) (DC)(DT)(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)(DT)(DA)(DT)(DA)(DC) (DA)(DT) (DC)(DC)(DT)(DG)(DT)(DT)(DC)(DC)(DA)(DG) (DT)(DG)(DC)(DC)(DG)(DG)(DT)(DG) (DT) (DC)(DG)(DC)(DG)(DA)(DT)

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Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / Number of copies: 4 / 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

Concentration0.1 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 3304 / Average electron dose: 44.01 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.6 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1394967
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4) / Number images used: 205635
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

3tu4

source_name: PDB, initial_model_type: experimental model

8h1t

source_name: PDB, initial_model_type: experimental model

8svf

source_name: PDB, initial_model_type: experimental model

4r8p

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL
Output model

PDB-9dgg:
ncPRC1RYBP bound to unmodified nucleosome

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