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- EMDB-17796: human RYBP-PRC1 bound to H2AK118ub1 nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-17796
Titlehuman RYBP-PRC1 bound to H2AK118ub1 nucleosome
Map dataFocused refine post-processing map
Sample
  • Complex: human RYBP-PRC1 bound to H2AK118ub1 nucleosome
    • Complex: human RYBP
      • Protein or peptide: RING1 and YY1-binding protein
    • 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)
    • Complex: Human Ubiquitin
      • Protein or peptide: Ubiquitin-40S ribosomal protein S27a (Fragment)
  • Ligand: ZINC ION
KeywordsncPRC1 / RYBP-PRC1 / nucleosome / H2A / histones / RYBP / Ubiquitin / K119 / GENE REGULATION
Function / homology
Function and homology information


Condensation of Prophase Chromosomes / Metalloprotease DUBs / E3 ubiquitin ligases ubiquitinate target proteins / RMTs methylate histone arginines / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / polytene chromosome band / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RNA Polymerase I Promoter Escape ...Condensation of Prophase Chromosomes / Metalloprotease DUBs / E3 ubiquitin ligases ubiquitinate target proteins / RMTs methylate histone arginines / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / polytene chromosome band / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RNA Polymerase I Promoter Escape / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / HDACs deacetylate histones / Ub-specific processing proteases / Regulation of endogenous retroelements by KRAB-ZFP proteins / larval somatic muscle development / Transcriptional regulation by small RNAs / Estrogen-dependent gene expression / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Senescence-Associated Secretory Phenotype (SASP) / HATs acetylate histones / UCH proteinases / Assembly of the ORC complex at the origin of replication / Oxidative Stress Induced Senescence / polytene chromosome / PcG protein complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Transcriptional Regulation by E2F6 / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / nucleosomal DNA binding / transcription coregulator activity / heterochromatin formation / structural constituent of chromatin / transcription corepressor activity / nucleosome / nucleosome assembly / chromatin organization / chromosome / nucleic acid binding / chromatin remodeling / positive regulation of apoptotic process / protein heterodimerization activity / regulation of DNA-templated transcription / protein-containing complex binding / apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Yaf2/RYBP C-terminal binding motif / RING1 and YY1-binding protein/YY1-associated factor 2 / Yaf2/RYBP C-terminal binding motif / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / S27a-like superfamily ...Yaf2/RYBP C-terminal binding motif / RING1 and YY1-binding protein/YY1-associated factor 2 / Yaf2/RYBP C-terminal binding motif / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / S27a-like superfamily / 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. / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Histone-fold / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Histone H4 / Histone H3 / Ubiquitin-40S ribosomal protein S27a / Histone H2B / Histone H2A / RING1 and YY1-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human) / Drosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 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) releaseApr 3, 2024-
Map releaseApr 3, 2024-
UpdateJul 31, 2024-
Current statusJul 31, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17796.png

Downloads & links

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Map

FileDownload / File: emd_17796.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused refine post-processing map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 224 pix.
= 245.056 Å		1.09 Å/pix.
x 224 pix.
= 245.056 Å		1.09 Å/pix.
x 224 pix.
= 245.056 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.094 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.04753726 - 0.087721474
Average (Standard dev.)0.000030584408 (±0.0036193836)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 245.056 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: non focused refine post-processing map

Fileemd_17796_additional_1.map
Annotationnon focused refine post-processing map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Focus refine half map

Fileemd_17796_half_map_1.map
AnnotationFocus refine half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Focus refine half map

Fileemd_17796_half_map_2.map
AnnotationFocus refine half map
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 H2AK118ub1 nucleosome

EntireName: human RYBP-PRC1 bound to H2AK118ub1 nucleosome
Components
  • Complex: human RYBP-PRC1 bound to H2AK118ub1 nucleosome
    • Complex: human RYBP
      • Protein or peptide: RING1 and YY1-binding protein
    • 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)
    • Complex: Human Ubiquitin
      • Protein or peptide: Ubiquitin-40S ribosomal protein S27a (Fragment)
  • Ligand: ZINC ION

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Supramolecule #1: human RYBP-PRC1 bound to H2AK118ub1 nucleosome

SupramoleculeName: human RYBP-PRC1 bound to H2AK118ub1 nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: human RYBP

SupramoleculeName: human RYBP / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #7
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: #1-#4
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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Supramolecule #4: DNA

SupramoleculeName: DNA / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #5: Human Ubiquitin

SupramoleculeName: Human Ubiquitin / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #8
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Histone H3 (Fragment)

MacromoleculeName: Histone H3 (Fragment) / type: protein_or_peptide / ID: 1 / 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 #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / 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 #3: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 3 / 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 #4: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 13.709027 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
IPPKTSGKAA KKAGKAQKNI TKTDKKKKRK RKESYAIYIY KVLKQVHPDT GISSKAMSIM NSFVNDIFER IAAEASRLAH YNKRSTITS REIQTAVRLL LPGELAKHAV SEGTKAVTKY TSSK

UniProtKB: Histone H2B

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Macromolecule #7: RING1 and YY1-binding protein

MacromoleculeName: RING1 and YY1-binding protein / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.219959 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GPDSMTMGDK KSPTRPKRQA KPAADEGFWD CSVCTFRNSA EAFKCSICDV RKGTSTRKPR INSQLVAQQV AQQYATPPPP KKEKKEKVE KQDKEKPEKD KEISPSVTKK NTNKKTKPKS DILKDPPSEA NSIQSANATT KTSETNHTSR PRLKNVDRST A QQLAVTVG ...String:
GPDSMTMGDK KSPTRPKRQA KPAADEGFWD CSVCTFRNSA EAFKCSICDV RKGTSTRKPR INSQLVAQQV AQQYATPPPP KKEKKEKVE KQDKEKPEKD KEISPSVTKK NTNKKTKPKS DILKDPPSEA NSIQSANATT KTSETNHTSR PRLKNVDRST A QQLAVTVG NVTVIITDFK EKTRSSSTSS STVTSSAGSE QQNQSSSGSE STDKGSSRSS TPKGDMSAVN DESF

UniProtKB: RING1 and YY1-binding protein

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Macromolecule #8: Ubiquitin-40S ribosomal protein S27a (Fragment)

MacromoleculeName: Ubiquitin-40S ribosomal protein S27a (Fragment) / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.305532 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRL

UniProtKB: Ubiquitin-40S ribosomal protein S27a

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Macromolecule #5: DNA (215-MER)

MacromoleculeName: DNA (215-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 76.456594 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) (DT)(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 #6: DNA (215-MER)

MacromoleculeName: DNA (215-MER) / type: dna / ID: 6 / 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 #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / Number of copies: 1 / 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 / Chamber humidity: 95 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 54.0 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: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL / In silico model: 3D initial model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12150042
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.1)

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