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- EMDB-46822: ncPRC1RYBP Delta-linker mutant bound to singly modified H2AK119Ub... -

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Basic information

Entry
Database: EMDB / ID: EMD-46822
TitlencPRC1RYBP Delta-linker mutant bound to singly modified H2AK119Ub nucleosome
Map dataOverall map of ncPRC1RYBP Delta-linker mutant bound to singly modified H2AK119Ub nucleosome
Sample
  • Complex: ncPRC1RYBP Delta-linker mutant bound to singly modified H2AK119Ub 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
    • Protein or peptide: Histone H2A type 1
    • DNA: DNA (187-MER)
    • DNA: DNA (187-MER)
    • Protein or peptide: RING1 and YY1-binding protein
    • Protein or peptide: Ubiquitin
  • Ligand: ZINC ION
KeywordsDNA complex protein / structural protein / NUCLEAR PROTEIN-DNA complex
Function / homology
Function and homology information


PcG protein complex / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / female gonad development / seminiferous tubule development / Transcriptional Regulation by E2F6 / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known ...PcG protein complex / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / female gonad development / seminiferous tubule development / Transcriptional Regulation by E2F6 / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / energy homeostasis / neuron projection morphogenesis / regulation of proteasomal protein catabolic process / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex / Prevention of phagosomal-lysosomal fusion / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / 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 / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / TRAF6-mediated induction of TAK1 complex within TLR4 complex / regulation of neuron apoptotic process / Downregulation of ERBB2:ERBB3 signaling / Regulation of innate immune responses to cytosolic DNA / Pexophagy / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / positive regulation of protein ubiquitination / TICAM1, RIP1-mediated IKK complex recruitment / Regulation of BACH1 activity / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Degradation of CDH1 / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Josephin domain DUBs / Downregulation of TGF-beta receptor signaling / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / Degradation of CRY and PER proteins / Regulation of activated PAK-2p34 by proteasome mediated degradation / PINK1-PRKN Mediated Mitophagy / regulation of mitochondrial membrane potential / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / TCF dependent signaling in response to WNT / Regulation of NF-kappa B signaling / APC/C:Cdc20 mediated degradation of Securin / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / transcription coregulator activity / activated TAK1 mediates p38 MAPK activation / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Regulation of signaling by CBL / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Assembly of the pre-replicative complex / Negative regulation of FGFR3 signaling / Fanconi Anemia Pathway / Peroxisomal protein import / Vpu mediated degradation of CD4 / Deactivation of the beta-catenin transactivating complex
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 / : ...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 / : / 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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Histone H2B 1.1 / Histone H2A type 1 / Polyubiquitin-B / Histone H4 / Histone H3.2 / RING1 and YY1-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.46 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 Institute of General Medical Sciences (NIH/NIGMS)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 1, 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_46822.png

Downloads & links

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Map

FileDownload / File: emd_46822.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOverall map of ncPRC1RYBP Delta-linker mutant bound to singly modified H2AK119Ub nucleosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.096 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.23
Minimum - Maximum0.0 - 1.3011264
Average (Standard dev.)0.007631463 (±0.047698762)
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_46822_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: DeepEMhancer sharpened map of ncPRC1RYBP Delta-linker mutant bound...

Fileemd_46822_additional_1.map
AnnotationDeepEMhancer sharpened map of ncPRC1RYBP Delta-linker mutant bound to singly modified H2AK119Ub nucleosome
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: Local filtered sharpened map of ncPRC1RYBP Delta-linker mutant...

Fileemd_46822_additional_2.map
AnnotationLocal filtered sharpened map of ncPRC1RYBP Delta-linker mutant bound to singly modified H2AK119Ub nucleosome, B-factor of -15
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of ncPRC1RYBP Delta-linker mutant bound...

Fileemd_46822_half_map_1.map
AnnotationHalf map A of ncPRC1RYBP Delta-linker mutant bound to singly modified H2AK119Ub nucleosome
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of ncPRC1RYBP Delta-linker mutant bound...

Fileemd_46822_half_map_2.map
AnnotationHalf map B of ncPRC1RYBP Delta-linker mutant bound to singly modified H2AK119Ub nucleosome
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 Delta-linker mutant bound to singly modified H2AK119Ub...

EntireName: ncPRC1RYBP Delta-linker mutant bound to singly modified H2AK119Ub nucleosome
Components
  • Complex: ncPRC1RYBP Delta-linker mutant bound to singly modified H2AK119Ub 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
    • Protein or peptide: Histone H2A type 1
    • DNA: DNA (187-MER)
    • DNA: DNA (187-MER)
    • Protein or peptide: RING1 and YY1-binding protein
    • Protein or peptide: Ubiquitin
  • Ligand: ZINC ION

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Supramolecule #1: ncPRC1RYBP Delta-linker mutant bound to singly modified H2AK119Ub...

SupramoleculeName: ncPRC1RYBP Delta-linker mutant bound to singly modified H2AK119Ub nucleosome
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
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: 1 / 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 #5: Histone H2A type 1

MacromoleculeName: Histone H2A type 1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / 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 #8: RING1 and YY1-binding protein

MacromoleculeName: RING1 and YY1-binding protein / type: protein_or_peptide / ID: 8 / 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 #9: Ubiquitin

MacromoleculeName: Ubiquitin / type: protein_or_peptide / ID: 9 / 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 #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: 57.982918 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 #7: DNA (187-MER)

MacromoleculeName: DNA (187-MER) / type: dna / ID: 7 / 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 #10: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 10 / 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

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 3292 / Average electron dose: 49.6 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1127632
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 23464
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
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

2d9g

source_name: PDB, initial_model_type: experimental model

1ubq

source_name: PDB, initial_model_type: experimental model

2wwz

source_name: PDB, initial_model_type: experimental model
Output model

PDB-9dg3:
ncPRC1RYBP Delta-linker mutant bound to singly modified H2AK119Ub nucleosome

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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