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- EMDB-46732: Overall map of ncPRC1RYBP bound to doubly modified H2AK119Ub nucl... -

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Basic information

Entry
Database: EMDB / ID: EMD-46732
TitleOverall map of ncPRC1RYBP bound to doubly modified H2AK119Ub nucleosome
Map dataOverall map of ncPRC1RYBP bound to doubly modified H2AK119Ub nucleosome, resampled in the direction Map 2
Sample
  • Complex: Overall map of ncPRC1RYBP bound to doubly modified H2AK119Ub nucleosome
    • Complex: Histones octamer
      • 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
      • Complex: Histone H2B 1.1
        • Protein or peptide: Histone H2B 1.1
    • Complex: DNA (187-MER)
      • 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, Ubiquitin-conjugating enzyme E2 D3
      • Complex: RING1 and YY1-binding protein
        • Protein or peptide: RING1 and YY1-binding protein
    • Complex: Ubiquitin
      • Protein or peptide: Ubiquitin
KeywordsDNA complex protein / hydrolase / structural protein / NUCLEAR PROTEIN-DNA complex / GENE REGULATION
Function / homology
Function and homology information


histone H2AK119 ubiquitin ligase activity / PRC1 complex / RING-like zinc finger domain binding / sex chromatin / PcG protein complex / SUMOylation of DNA methylation proteins / gastrulation with mouth forming second / SUMOylation of RNA binding proteins / anterior/posterior axis specification / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known ...histone H2AK119 ubiquitin ligase activity / PRC1 complex / RING-like zinc finger domain binding / sex chromatin / PcG protein complex / SUMOylation of DNA methylation proteins / gastrulation with mouth forming second / SUMOylation of RNA binding proteins / anterior/posterior axis specification / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Transcriptional Regulation by E2F6 / germ cell development / MLL1 complex / ubiquitin ligase complex / SUMOylation of DNA damage response and repair proteins / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / 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 / transcription coregulator activity / euchromatin / RING-type E3 ubiquitin transferase / transcription corepressor activity / structural constituent of chromatin / ubiquitin protein ligase activity / nucleosome / heterochromatin formation / mitotic cell cycle / Oxidative Stress Induced Senescence / gene expression / nucleic acid binding / protein ubiquitination / nuclear body / positive regulation of apoptotic process / chromatin remodeling / protein heterodimerization activity / apoptotic process / chromatin binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / 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 / 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 domain / Zn-finger in Ran binding protein and others ...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 / Zinc finger, C3HC4 type (RING finger) / 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 / 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 / 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: 3.41 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 24, 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_46732.png

Downloads & links

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Map

FileDownload / File: emd_46732.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOverall map of ncPRC1RYBP bound to doubly modified H2AK119Ub nucleosome, resampled in the direction Map 2
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 - Maximum-0.22955766 - 1.200838
Average (Standard dev.)0.0050601987 (±0.053106904)
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_46732_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Half map B of ncPRC1RYBP bound to doubly...

Fileemd_46732_additional_1.map
AnnotationHalf map B of ncPRC1RYBP bound to doubly modified H2AK119Ub nucleosome, without resampling
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpen map of ncPRC1RYBP bound to doubly modified...

Fileemd_46732_additional_2.map
AnnotationSharpen map of ncPRC1RYBP bound to doubly modified H2AK119Ub nucleosome, without resampling
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map of ncPRC1RYBP bound to doubly modified...

Fileemd_46732_additional_3.map
AnnotationSharpened map of ncPRC1RYBP bound to doubly modified H2AK119Ub nucleosome, resampled in the direction Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Raw overall map of ncPRC1RYBP bound to doubly...

Fileemd_46732_additional_4.map
AnnotationRaw overall map of ncPRC1RYBP bound to doubly modified H2AK119Ub nucleosome, without resampling
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Half map A of ncPRC1RYBP bound to doubly...

Fileemd_46732_additional_5.map
AnnotationHalf map A of ncPRC1RYBP bound to doubly modified H2AK119Ub nucleosome, without resampling
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 doubly...

Fileemd_46732_half_map_1.map
AnnotationHalf map B of ncPRC1RYBP bound to doubly modified H2AK119Ub nucleosome, resampled in the direction Map 2
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 doubly...

Fileemd_46732_half_map_2.map
AnnotationHalf map A of ncPRC1RYBP bound to doubly modified H2AK119Ub nucleosome, resampled in the direction Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Overall map of ncPRC1RYBP bound to doubly modified H2AK119Ub nucl...

EntireName: Overall map of ncPRC1RYBP bound to doubly modified H2AK119Ub nucleosome
Components
  • Complex: Overall map of ncPRC1RYBP bound to doubly modified H2AK119Ub nucleosome
    • Complex: Histones octamer
      • 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
      • Complex: Histone H2B 1.1
        • Protein or peptide: Histone H2B 1.1
    • Complex: DNA (187-MER)
      • 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, Ubiquitin-conjugating enzyme E2 D3
      • Complex: RING1 and YY1-binding protein
        • Protein or peptide: RING1 and YY1-binding protein
    • Complex: Ubiquitin
      • Protein or peptide: Ubiquitin

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Supramolecule #1: Overall map of ncPRC1RYBP bound to doubly modified H2AK119Ub nucl...

SupramoleculeName: Overall map of ncPRC1RYBP bound to doubly modified H2AK119Ub nucleosome
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Histones octamer

SupramoleculeName: Histones octamer / 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 (187-MER)

SupramoleculeName: DNA (187-MER) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: synthetic construct (others)

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Supramolecule #4: Histone H3.2

SupramoleculeName: Histone H3.2 / type: complex / ID: 4 / Parent: 2 / Macromolecule list: #1
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Supramolecule #5: DNA (187-MER)

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

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Supramolecule #6: ncPRC1-RYBP

SupramoleculeName: ncPRC1-RYBP / type: complex / ID: 6 / Parent: 1 / Macromolecule list: #7-#9
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #7: Ubiquitin

SupramoleculeName: Ubiquitin / type: complex / ID: 7 / Parent: 1 / Macromolecule list: #10
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #8: Histone H4

SupramoleculeName: Histone H4 / type: complex / ID: 8 / Parent: 2 / Macromolecule list: #2
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Supramolecule #9: Histone H2A

SupramoleculeName: Histone H2A / type: complex / ID: 9 / Parent: 2 / Macromolecule list: #3
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Supramolecule #10: Histone H2B 1.1

SupramoleculeName: Histone H2B 1.1 / type: complex / ID: 10 / Parent: 2 / Macromolecule list: #4
Source (natural)Organism: Xenopus laevis (African clawed frog)

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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: 6 / 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: 6 / 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: 6 / Macromolecule list: #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 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSAV MALQEASEAY LVALFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3.2

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

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Macromolecule #3: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKQGGK TRAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAVRN DEELNKLLGR VTIAQGGVLP NIQSVLLPCK TESAKSAKSK

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 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPEPAKSAPA PKKGSKKAVT KTQKKDGKKR RKTRKESYAI YVYKVLKQVH PDTGISSKAM SIMNSFVNDV FERIAGEASR LAHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSAK

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 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
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: Histone H2A type 1

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Macromolecule #8: E3 ubiquitin-protein ligase RING2, Ubiquitin-conjugating enzyme E2 D3

MacromoleculeName: E3 ubiquitin-protein ligase RING2, Ubiquitin-conjugating enzyme E2 D3
type: protein_or_peptide / ID: 8 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
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 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
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 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGC

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Macromolecule #5: DNA (187-MER)

MacromoleculeName: DNA (187-MER) / type: dna / ID: 5 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
SequenceString:
atcgcgacac cggcactgga acaggatgta tatatctgac acgtgcctgg agactaggga gtaatcccct tggcggttaa aacgcggggg acagcgcgta cgtgcgttta agcggtgcta gagctgtcta cgaccaattg agcggcctcg gcaccgggat tctccagggg atcgggcatc acccgat

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Macromolecule #6: DNA (187-MER)

MacromoleculeName: DNA (187-MER) / type: dna / ID: 6 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
SequenceString:
atcgggtgat gcccgatccc ctggagaatc ccggtgccga ggccgctcaa ttggtcgtag acagctctag caccgcttaa acgcacgtac gcgctgtccc ccgcgtttta accgccaagg ggattactcc ctagtctcca ggcacgtgtc agatatatac atcctgttcc agtgccggtg tcgcgat

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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: 1969 / Average electron dose: 50.92 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2213782
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.4.1) / Number images used: 43857
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. v4.4.1)
Final 3D classificationSoftware - Name: cryoSPARC (ver. v4.4.1)
FSC plot (resolution estimation)

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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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