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- EMDB-17797: human RYBP-PRC1 bound to mononucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-17797
Titlehuman RYBP-PRC1 bound to mononucleosome
Map dataSharpened map
Sample
  • Complex: human RYBP-PRC1 bound to nucleosome
    • Complex: RING1B:BMI1 heterodimer
      • Protein or peptide: Polycomb complex protein BMI-1
      • Protein or peptide: E3 ubiquitin-protein ligase RING2
    • Complex: Drosophila octamer
      • Protein or peptide: Histone H3 (Fragment)
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B
    • Complex: DNA
      • DNA: DNA (215-mer)
      • DNA: DNA (215-mer)
  • Ligand: ZINC ION
KeywordsncPRC1 complex / nucleosome / H2A / histones / RING1B / BMI1 / heterodimer / E3 ligase / K119 / GENE REGULATION
Function / homology
Function and homology information


histone H2AK119 ubiquitin ligase activity / regulation of adaxial/abaxial pattern formation / E3 ubiquitin ligases ubiquitinate target proteins / polytene chromosome band / HATs acetylate histones / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Ub-specific processing proteases / larval somatic muscle development / rostrocaudal neural tube patterning / RING-like zinc finger domain binding ...histone H2AK119 ubiquitin ligase activity / regulation of adaxial/abaxial pattern formation / E3 ubiquitin ligases ubiquitinate target proteins / polytene chromosome band / HATs acetylate histones / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Ub-specific processing proteases / larval somatic muscle development / rostrocaudal neural tube patterning / RING-like zinc finger domain binding / sex chromatin / PRC1 complex / segment specification / ubiquitin-protein transferase activator activity / somatic stem cell division / embryonic skeletal system morphogenesis / polytene chromosome / PcG protein complex / positive regulation of immature T cell proliferation in thymus / SUMOylation of DNA methylation proteins / gastrulation with mouth forming second / SUMOylation of RNA binding proteins / positive regulation of ubiquitin-protein transferase activity / anterior/posterior axis specification / 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 / MLL1 complex / negative regulation of apoptotic signaling pathway / humoral immune response / hemopoiesis / heterochromatin / ubiquitin ligase complex / epigenetic regulation of gene expression / SUMOylation of DNA damage response and repair proteins / positive regulation of B cell proliferation / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / Regulation of PTEN gene transcription / promoter-specific chromatin binding / apoptotic signaling pathway / brain development / euchromatin / RING-type E3 ubiquitin transferase / negative regulation of DNA-binding transcription factor activity / nucleosome assembly / structural constituent of chromatin / ubiquitin protein ligase activity / positive regulation of fibroblast proliferation / nucleosome / mitotic cell cycle / chromosome / gene expression / chromatin organization / regulation of gene expression / Oxidative Stress Induced Senescence / in utero embryonic development / protein ubiquitination / nuclear body / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / chromatin binding / protein-containing complex 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. / Histone H2B ...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 / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Zinc finger RING-type profile. / Zinc finger, RING-type / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Histone H4 / Histone H3 / Histone H2B / Polycomb complex protein BMI-1 / Histone H2A / E3 ubiquitin-protein ligase RING2
Similarity search - Component
Biological speciesHomo sapiens (human) / Drosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsCiapponi M / Benda C / Mueller J
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Structural basis of the histone ubiquitination read-write mechanism of RYBP-PRC1.
Authors: Maria Ciapponi / Elena Karlukova / Sven Schkölziger / Christian Benda / Jürg Müller /
Abstract: Histone H2A monoubiquitination (H2Aub1) by the PRC1 subunit RING1B entails a positive feedback loop, mediated by the RING1B-interacting protein RYBP. We uncover that human RYBP-PRC1 binds unmodified ...Histone H2A monoubiquitination (H2Aub1) by the PRC1 subunit RING1B entails a positive feedback loop, mediated by the RING1B-interacting protein RYBP. We uncover that human RYBP-PRC1 binds unmodified nucleosomes via RING1B but H2Aub1-modified nucleosomes via RYBP. RYBP interactions with both ubiquitin and the nucleosome acidic patch create the high binding affinity that favors RYBP- over RING1B-directed PRC1 binding to H2Aub1-modified nucleosomes; this enables RING1B to monoubiquitinate H2A in neighboring unmodified nucleosomes.
History
DepositionJul 6, 2023-
Header (metadata) releaseMar 27, 2024-
Map releaseMar 27, 2024-
UpdateApr 3, 2024-
Current statusApr 3, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17797.png

Downloads & links

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Map

FileDownload / File: emd_17797.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 280 pix.
= 238. Å		0.85 Å/pix.
x 280 pix.
= 238. Å		0.85 Å/pix.
x 280 pix.
= 238. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.0283144 - 2.01102
Average (Standard dev.)0.00297312 (±0.06992465)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 238.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_17797_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_17797_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : human RYBP-PRC1 bound to nucleosome

EntireName: human RYBP-PRC1 bound to nucleosome
Components
  • Complex: human RYBP-PRC1 bound to nucleosome
    • Complex: RING1B:BMI1 heterodimer
      • Protein or peptide: Polycomb complex protein BMI-1
      • Protein or peptide: E3 ubiquitin-protein ligase RING2
    • Complex: Drosophila octamer
      • Protein or peptide: Histone H3 (Fragment)
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B
    • Complex: DNA
      • DNA: DNA (215-mer)
      • DNA: DNA (215-mer)
  • Ligand: ZINC ION

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Supramolecule #1: human RYBP-PRC1 bound to nucleosome

SupramoleculeName: human RYBP-PRC1 bound to nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: RING1B:BMI1 heterodimer

SupramoleculeName: RING1B:BMI1 heterodimer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Drosophila octamer

SupramoleculeName: Drosophila octamer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#6
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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Supramolecule #4: DNA

SupramoleculeName: DNA / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #7-#8
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Polycomb complex protein BMI-1

MacromoleculeName: Polycomb complex protein BMI-1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.152359 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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 GMKHHHHHH

UniProtKB: Polycomb complex protein BMI-1

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Macromolecule #2: E3 ubiquitin-protein ligase RING2

MacromoleculeName: E3 ubiquitin-protein ligase RING2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.062707 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GPDSMSQAVQ TNGTQPLSKT WELSLYELQR TPQEAITDGL EIVVSPRSLH SELMCPICLD MLKNTMTTKE CLHRFCADCI ITALRSGNK ECPTCRKKLV SKRSLRPDPN FDALISKIYP SRDEYEAHQE RVLARINKHN NQQALSHSIE EGLKIQAMNR L QRGKKQQI ...String:
GPDSMSQAVQ TNGTQPLSKT WELSLYELQR TPQEAITDGL EIVVSPRSLH SELMCPICLD MLKNTMTTKE CLHRFCADCI ITALRSGNK ECPTCRKKLV SKRSLRPDPN FDALISKIYP SRDEYEAHQE RVLARINKHN NQQALSHSIE EGLKIQAMNR L QRGKKQQI ENGSGAEDNG DSSHCSNAST HSNQEAGPSN KRTKTSDDSG LELDNNNAAM AIDPVMDGAS EIELVFRPHP TL MEKDDSA QTRYIKTSGN ATVDHLSKYL AVRLALEELR SKGESNQMNL DTASEKQYTI YIATASGQFT VLNGSFSLEL VSE KYWKVN KPMELYYAPT KEHK

UniProtKB: E3 ubiquitin-protein ligase RING2

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Macromolecule #3: Histone H3 (Fragment)

MacromoleculeName: Histone H3 (Fragment) / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 15.289904 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEASEAY LVGLFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3

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Macromolecule #4: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 11.521611 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MITGRGKGGK GLGKGGAKRH RKVLRDNIQG ITKPAIRRLA RRGGVKRISG LIYEETRGVL KVFLENVIRD AVTYTEHAKR KTVTAMDVV YALKRQGRTL YGFGG

UniProtKB: Histone H4

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Macromolecule #5: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 13.257529 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKGGKVK GKAKSRSNRA GLQFPVGRIH RLLRKGNYAE RVGAGAPVYL AAVMEYLAAE VLELAGNAAR DNKKTRIIPR HLQLAIRND EELNKLLSGV TIAQGGVLPN IQAVLLPKKT EKKA

UniProtKB: Histone H2A

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Macromolecule #6: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 13.727064 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPPKTSGKAA KKAGKAQKNI TKTDKKKKRK RKESYAIYIY KVLKQVHPDT GISSKAMSIM NSFVNDIFER IAAEASRLAH YNKRSTITS REIQTAVRLL LPGELAKHAV SEGTKAVTKY TSSK

UniProtKB: Histone H2B

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Macromolecule #7: DNA (215-mer)

MacromoleculeName: DNA (215-mer) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 76.716836 KDa
SequenceString: (DC)(DC)(DA)(DA)(DG)(DC)(DT)(DT)(DG)(DC) (DA)(DT)(DG)(DC)(DC)(DT)(DG)(DC)(DA)(DG) (DG)(DT)(DC)(DG)(DA)(DC)(DT)(DC)(DT) (DA)(DG)(DA)(DG)(DA)(DT)(DA)(DT)(DC)(DC) (DC) (DG)(DA)(DG)(DT)(DC)(DG) ...String:
(DC)(DC)(DA)(DA)(DG)(DC)(DT)(DT)(DG)(DC) (DA)(DT)(DG)(DC)(DC)(DT)(DG)(DC)(DA)(DG) (DG)(DT)(DC)(DG)(DA)(DC)(DT)(DC)(DT) (DA)(DG)(DA)(DG)(DA)(DT)(DA)(DT)(DC)(DC) (DC) (DG)(DA)(DG)(DT)(DC)(DG)(DC)(DT) (DG)(DT)(DT)(DC)(DA)(DA)(DT)(DA)(DA)(DA) (DT)(DA) (DC)(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)(DT)(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)(DT) (DC)(DC)(DG)(DC)(DC)(DG)(DC)(DG)(DT)(DA) (DT)(DA)(DG)(DG)(DG)(DT)(DC)(DC)(DA) (DT)(DC)(DA)(DC)(DA)(DT)(DA)(DA)(DG)(DC) (DC) (DC)(DG)(DA)(DG)(DA)(DT)(DA)(DT)

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Macromolecule #8: DNA (215-mer)

MacromoleculeName: DNA (215-mer) / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 76.481609 KDa
SequenceString: (DA)(DT)(DA)(DT)(DC)(DT)(DC)(DG)(DG)(DG) (DC)(DT)(DT)(DA)(DT)(DG)(DT)(DG)(DA)(DT) (DG)(DG)(DA)(DC)(DC)(DC)(DT)(DA)(DT) (DA)(DC)(DG)(DC)(DG)(DG)(DC)(DG)(DG)(DA) (DC) (DC)(DT)(DG)(DG)(DA)(DG) ...String:
(DA)(DT)(DA)(DT)(DC)(DT)(DC)(DG)(DG)(DG) (DC)(DT)(DT)(DA)(DT)(DG)(DT)(DG)(DA)(DT) (DG)(DG)(DA)(DC)(DC)(DC)(DT)(DA)(DT) (DA)(DC)(DG)(DC)(DG)(DG)(DC)(DG)(DG)(DA) (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)(DG)(DT)(DA)(DT) (DG)(DT)(DA)(DT)(DT)(DG)(DA)(DA)(DC) (DA)(DG)(DC)(DG)(DA)(DC)(DT)(DC)(DG)(DG) (DG)(DA)(DT)(DA)(DT)(DC)(DT)(DC)(DT)(DA) (DG)(DA)(DG)(DT)(DC)(DG)(DA)(DC)(DC) (DT)(DG)(DC)(DA)(DG)(DG)(DC)(DA)(DT)(DG) (DC) (DA)(DA)(DG)(DC)(DT)(DT)(DG)(DG)

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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
GridMaterial: COPPER
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.6 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL / In silico model: Ab initio reconstruction
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 146136

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