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- EMDB-46771: ncPRC1RYBP bound to H2AK119Ub/H1.4 chromatosome -

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Basic information

Entry
Database: EMDB / ID: EMD-46771
TitlencPRC1RYBP bound to H2AK119Ub/H1.4 chromatosome
Map dataOverall map of ncPRC1RYBP bound to H2AK119Ub/H1.4 chromatosome
Sample
  • Complex: ncPRC1RYBP bound to H2AK119Ub/H1.4 Chromatosome
    • Complex: Histones
      • Complex: Histone H3.2
        • Protein or peptide: x 1 types
      • Complex: Histone H4
        • Protein or peptide: x 1 types
      • Complex: Histone H2A
        • Protein or peptide: x 1 types
      • Complex: Histone H2B 1.1
        • Protein or peptide: x 1 types
    • Complex: DNA
      • Complex: DNA (187-MER)
        • DNA: x 1 types
      • Complex: DNA (187-MER)
        • DNA: x 1 types
    • Complex: ncPRC1-RYBP
      • Complex: Polycomb complex protein BMI-1
        • Protein or peptide: x 1 types
      • Complex: E3 ubiquitin-protein ligase RING2, Ubiquitin-conjugating enzyme E2 D3
        • Protein or peptide: x 1 types
      • Complex: RING1 and YY1-binding protein
        • Protein or peptide: x 1 types
    • Complex: Ubiquitin
      • Protein or peptide: x 1 types
    • Complex: Histone H1.4
      • Protein or peptide: x 1 types
  • Ligand: x 1 types
KeywordsDNA complex protein / Gene Regulation-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 / negative regulation of DNA recombination / SUMOylation of DNA methylation proteins / Apoptosis induced DNA fragmentation / gastrulation with mouth forming second / SUMOylation of RNA binding proteins / chromosome condensation / hypothalamus gonadotrophin-releasing hormone neuron development / anterior/posterior axis specification / female meiosis I / positive regulation of protein monoubiquitination / positive regulation of ubiquitin-protein transferase activity / nucleosomal DNA binding / fat pad development / mitochondrion transport along microtubule / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / DNA methylation-dependent constitutive heterochromatin formation / female gonad development / seminiferous tubule development / negative regulation of gene expression, epigenetic / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Transcriptional Regulation by E2F6 / male meiosis I / germ cell development / hemopoiesis / humoral immune response / negative regulation of apoptotic signaling pathway / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / MLL1 complex / cellular response to interleukin-1 / ubiquitin ligase complex / heterochromatin / SUMOylation of DNA damage response and repair proteins / energy homeostasis / regulation of neuron apoptotic process / positive regulation of B cell proliferation / regulation of proteasomal protein catabolic process / Maturation of protein E / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / cellular response to dexamethasone stimulus / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / Regulation of PTEN localization / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / neuron projection morphogenesis / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / regulation of mitochondrial membrane potential / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / epigenetic regulation of gene expression
Similarity search - Function
Yaf2/RYBP C-terminal binding motif / RING1 and YY1-binding protein/YY1-associated factor 2 / Yaf2/RYBP C-terminal binding motif / E3 ubiquitin-protein ligase RING2 / E3 ubiquitin-protein ligase RING1/RING2 / RAWUL domain / RAWUL domain RING finger- and WD40-associated ubiquitin-like / Linker histone H1/H5 / linker histone H1 and H5 family / Zinc finger, C3HC4 type (RING finger) ...Yaf2/RYBP C-terminal binding motif / RING1 and YY1-binding protein/YY1-associated factor 2 / Yaf2/RYBP C-terminal binding motif / E3 ubiquitin-protein ligase RING2 / E3 ubiquitin-protein ligase RING1/RING2 / RAWUL domain / RAWUL domain RING finger- and WD40-associated ubiquitin-like / Linker histone H1/H5 / linker histone H1 and H5 family / Zinc finger, C3HC4 type (RING finger) / Linker histone H1/H5, domain H15 / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 / 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 / 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 / : / Ubiquitin domain signature. / Histone H2A/H2B/H3 / Ubiquitin conserved site / Core histone H2A/H2B/H3/H4 / Ubiquitin domain / Histone-fold / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Histone H2B 1.1 / Histone H2A type 1 / Polyubiquitin-B / Histone H1.4 / Polycomb complex protein BMI-1 / Histone H4 / Histone H3.2 / RING1 and YY1-binding protein / 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: 3.2 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
DepositionAug 28, 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_46771.png

Downloads & links

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Map

FileDownload / File: emd_46771.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOverall map of ncPRC1RYBP bound to H2AK119Ub/H1.4 chromatosome
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 360 pix.
= 389.88 Å		1.08 Å/pix.
x 360 pix.
= 389.88 Å		1.08 Å/pix.
x 360 pix.
= 389.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.083 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum0.0 - 2.521205
Average (Standard dev.)0.006474639 (±0.058527343)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 389.87997 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened map of ncPRC1RYBP bound to H2AK119Ub/H1.4 chromatosome,...

Fileemd_46771_additional_1.map
AnnotationSharpened map of ncPRC1RYBP bound to H2AK119Ub/H1.4 chromatosome, B-factor of -90
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: DeepEMhancer sharpened map of ncPRC1RYBP bound to H2AK119Ub/H1.4...

Fileemd_46771_additional_2.map
AnnotationDeepEMhancer sharpened map of ncPRC1RYBP bound to H2AK119Ub/H1.4 chromatosome
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of ncPRC1RYBP bound to H2AK119Ub/H1.4 chromatosome

Fileemd_46771_half_map_1.map
AnnotationHalf map A of ncPRC1RYBP bound to H2AK119Ub/H1.4 chromatosome
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of ncPRC1RYBP bound to H2AK119Ub/H1.4 chromatosome

Fileemd_46771_half_map_2.map
AnnotationHalf map B of ncPRC1RYBP bound to H2AK119Ub/H1.4 chromatosome
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ncPRC1RYBP bound to H2AK119Ub/H1.4 Chromatosome

EntireName: ncPRC1RYBP bound to H2AK119Ub/H1.4 Chromatosome
Components
  • Complex: ncPRC1RYBP bound to H2AK119Ub/H1.4 Chromatosome
    • Complex: Histones
      • Complex: Histone H3.2
        • Protein or peptide: Histone H3.2
      • Complex: Histone H4
        • Protein or peptide: Histone H4
      • Complex: Histone H2A
        • Protein or peptide: Histone H2A type 1
      • Complex: Histone H2B 1.1
        • Protein or peptide: Histone H2B 1.1
    • Complex: DNA
      • Complex: DNA (187-MER)
        • DNA: DNA (187-MER)
      • Complex: DNA (187-MER)
        • DNA: DNA (187-MER)
    • Complex: ncPRC1-RYBP
      • Complex: Polycomb complex protein BMI-1
        • Protein or peptide: Polycomb complex protein BMI-1
      • Complex: E3 ubiquitin-protein ligase RING2, Ubiquitin-conjugating enzyme E2 D3
        • Protein or peptide: E3 ubiquitin-protein ligase RING2
      • Complex: RING1 and YY1-binding protein
        • Protein or peptide: RING1 and YY1-binding protein
    • Complex: Ubiquitin
      • Protein or peptide: Ubiquitin
    • Complex: Histone H1.4
      • Protein or peptide: Histone H1.4
  • Ligand: ZINC ION

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Supramolecule #1: ncPRC1RYBP bound to H2AK119Ub/H1.4 Chromatosome

SupramoleculeName: ncPRC1RYBP bound to H2AK119Ub/H1.4 Chromatosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Histones

SupramoleculeName: Histones / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Supramolecule #3: DNA

SupramoleculeName: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: synthetic construct (others)

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Supramolecule #4: ncPRC1-RYBP

SupramoleculeName: ncPRC1-RYBP / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #7-#9
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #5: Ubiquitin

SupramoleculeName: Ubiquitin / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #10
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #6: Histone H3.2

SupramoleculeName: Histone H3.2 / type: complex / ID: 6 / Parent: 2 / Macromolecule list: #1
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Supramolecule #7: Histone H4

SupramoleculeName: Histone H4 / type: complex / ID: 7 / Parent: 2 / Macromolecule list: #2
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Supramolecule #8: Histone H2A

SupramoleculeName: Histone H2A / type: complex / ID: 8 / Parent: 2 / Macromolecule list: #3
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Supramolecule #9: Histone H2B 1.1

SupramoleculeName: Histone H2B 1.1 / type: complex / ID: 9 / Parent: 2 / Macromolecule list: #4
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Supramolecule #10: DNA (187-MER)

SupramoleculeName: DNA (187-MER) / type: complex / ID: 10 / Parent: 3 / Macromolecule list: #5
Source (natural)Organism: synthetic construct (others)

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Supramolecule #11: DNA (187-MER)

SupramoleculeName: DNA (187-MER) / type: complex / ID: 11 / Parent: 3 / Macromolecule list: #6
Source (natural)Organism: synthetic construct (others)

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Supramolecule #12: Polycomb complex protein BMI-1

SupramoleculeName: Polycomb complex protein BMI-1 / type: complex / ID: 12 / Parent: 4 / Macromolecule list: #7
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #13: E3 ubiquitin-protein ligase RING2, Ubiquitin-conjugating enzyme E2 D3

SupramoleculeName: E3 ubiquitin-protein ligase RING2, Ubiquitin-conjugating enzyme E2 D3
type: complex / ID: 13 / Parent: 4 / Macromolecule list: #8
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #14: RING1 and YY1-binding protein

SupramoleculeName: RING1 and YY1-binding protein / type: complex / ID: 14 / Parent: 4 / Macromolecule list: #9
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #15: Histone H1.4

SupramoleculeName: Histone H1.4 / type: complex / ID: 15 / Parent: 1 / Macromolecule list: #11
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: 14.067398 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKQGGK TRAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAVR NDEELNKLLG RVTIAQGGVL PNIQSVLLPC 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 #9: RING1 and YY1-binding protein

MacromoleculeName: RING1 and YY1-binding protein / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.863625 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTMGDKKSPT RPKRQAKPAA DEGFWDCSVC TFRNSAEAFK CSICDVRKGT STRKPRINSQ LVAQQVAQQY ATPPPPKKEK KEKVEKQDK EKPEKDKEIS PSVTKKNTNK KTKPKSDILK DPPSEANSIQ SANATTKTSE TNHTSRPRLK NVDRSTAQQL A VTVGNVTV ...String:
MTMGDKKSPT RPKRQAKPAA DEGFWDCSVC TFRNSAEAFK CSICDVRKGT STRKPRINSQ LVAQQVAQQY ATPPPPKKEK KEKVEKQDK EKPEKDKEIS PSVTKKNTNK KTKPKSDILK DPPSEANSIQ SANATTKTSE TNHTSRPRLK NVDRSTAQQL A VTVGNVTV IITDFKEKTR SSSTSSSTVT SSAGSEQQNQ SSSGSESTDK GSSRSSTPKG DMSAVNDESF

UniProtKB: RING1 and YY1-binding protein

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Macromolecule #10: Ubiquitin

MacromoleculeName: Ubiquitin / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.622922 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGC

UniProtKB: Polyubiquitin-B

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Macromolecule #11: Histone H1.4

MacromoleculeName: Histone H1.4 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.931521 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSETAPAAPA APAPAEKTPV KKKARKSAGA AKRKASGPPV SELITKAVAA SKERSGVSLA ALKKALAAAG YDVEKNNSRI KLGLKSLVS KGTLVQTKGT GASGSFKLNK KAASGEAKPK AKKAGAAKAK KPAGAAKKPK KATGAATPKK SAKKTPKKAK K PAAAAGAK ...String:
MSETAPAAPA APAPAEKTPV KKKARKSAGA AKRKASGPPV SELITKAVAA SKERSGVSLA ALKKALAAAG YDVEKNNSRI KLGLKSLVS KGTLVQTKGT GASGSFKLNK KAASGEAKPK AKKAGAAKAK KPAGAAKKPK KATGAATPKK SAKKTPKKAK K PAAAAGAK KAKSPKKAKA AKPKKAPKSP AKAKAVKPKA AKPKTAKPKA AKPKKAAAKK K

UniProtKB: Histone H1.4

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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)

+
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)

+
Macromolecule #12: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 12 / Number of copies: 5 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 7820 / Average electron dose: 61.06 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1394967
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 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
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
ChainDetailsPDB ID
source_name: AlphaFold, initial_model_type: in silico modelMultimer prediction
source_name: PDB, initial_model_type: experimental model

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

2d9g

source_name: SwissModel, initial_model_type: in silico modelSwissModelTemplate
source_name: PDB, initial_model_type: experimental model

1ubq

source_name: PDB, initial_model_type: experimental model

7pfv

RefinementSpace: REAL
Output model

PDB-9dde:
ncPRC1RYBP bound to H2AK119Ub/H1.4 chromatosome

-
Atomic model buiding 2

Initial modelPDB ID:

2wwz


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9dde:
ncPRC1RYBP bound to H2AK119Ub/H1.4 chromatosome

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