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- EMDB-56669: Human PRC1.4 in complex with native UBCH5C bound to a H3Kc27me3 m... -

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Basic information

Entry
Database: EMDB / ID: EMD-56669
TitleHuman PRC1.4 in complex with native UBCH5C bound to a H3Kc27me3 mononucleosome
Map datasharpened map
Sample
  • Complex: Human PRC1.4 in complex with native UBCH5C bound to a H3Kc27me3 mononucleosome
    • Protein or peptide: x 9 types
    • DNA: x 2 types
  • Ligand: x 1 types
KeywordsPRC1 / PRC1.4 / nucleosome / UBCH5C / GENE REGULATION / H3Kc27me3
Function / homology
Function and homology information


histone H2AK119 ubiquitin ligase activity / segment specification / RING-like zinc finger domain binding / ubiquitin-protein transferase activator activity / positive regulation of immature T cell proliferation in thymus / sex chromatin / germ cell development / PcG protein complex / PRC1 complex / (E3-independent) E2 ubiquitin-conjugating enzyme ...histone H2AK119 ubiquitin ligase activity / segment specification / RING-like zinc finger domain binding / ubiquitin-protein transferase activator activity / positive regulation of immature T cell proliferation in thymus / sex chromatin / germ cell development / PcG protein complex / PRC1 complex / (E3-independent) E2 ubiquitin-conjugating enzyme / SUMOylation of DNA methylation proteins / SUMOylation of RNA binding proteins / protein K11-linked ubiquitination / protein K6-linked ubiquitination / Differentiation of naive CD4+ T cells to T helper 2 cells (Th2 cells) / positive regulation of ubiquitin-protein transferase activity / E2 ubiquitin-conjugating enzyme / negative regulation of gene expression, epigenetic / hemopoiesis / Transcriptional Regulation by E2F6 / ubiquitin conjugating enzyme activity / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / MLL1 complex / positive regulation of B cell proliferation / SUMOylation of DNA damage response and repair proteins / ubiquitin ligase complex / heterochromatin / protein K48-linked ubiquitination / SUMOylation of transcription cofactors / positive regulation of fibroblast proliferation / Regulation of PTEN gene transcription / SUMOylation of chromatin organization proteins / promoter-specific chromatin binding / epigenetic regulation of gene expression / euchromatin / RING-type E3 ubiquitin transferase / nucleosomal DNA binding / protein polyubiquitination / ubiquitin-protein transferase activity / regulation of gene expression / structural constituent of chromatin / nucleosome / ubiquitin protein ligase activity / nucleosome assembly / heterochromatin formation / histone binding / Oxidative Stress Induced Senescence / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear body / endosome membrane / protein ubiquitination / chromatin remodeling / ribonucleoprotein complex / protein heterodimerization activity / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / DNA-templated transcription / DNA binding / nucleoplasm / zinc ion binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Unstructured region on Polyhomeotic-like protein 1 and 2 / Zinc finger, FCS-type / FCS-type zinc finger superfamily / Chromobox protein homolog 7 / Zinc finger, FCS-type / Zinc finger FCS-type profile. / CBX family C-terminal motif / CBX family C-terminal motif / E3 ubiquitin-protein ligase RING2 / E3 ubiquitin-protein ligase RING1/RING2 ...Unstructured region on Polyhomeotic-like protein 1 and 2 / Zinc finger, FCS-type / FCS-type zinc finger superfamily / Chromobox protein homolog 7 / Zinc finger, FCS-type / Zinc finger FCS-type profile. / CBX family C-terminal motif / CBX family C-terminal motif / E3 ubiquitin-protein ligase RING2 / E3 ubiquitin-protein ligase RING1/RING2 / RAWUL domain / RAWUL domain RING finger- and WD40-associated ubiquitin-like / : / Chromo domain subgroup / linker histone H1 and H5 family / Linker histone H1/H5, domain H15 / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 / Zinc finger, C3HC4 type (RING finger) / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / SAM domain (Sterile alpha motif) / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / : / 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 / Zinc finger RING-type profile. / Zinc finger, RING-type / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Histone H2B / Histone H3 / Chromobox 7 / Polycomb complex protein BMI-1 / Histone H4 / Ubiquitin-conjugating enzyme E2 D3 / Histone H2A / Polyhomeotic-like protein 2 / E3 ubiquitin-protein ligase RING2
Similarity search - Component
Biological speciesHomo sapiens (human) / Xenopus (frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.74 Å
AuthorsCiapponi M / Mueller J
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2026
Title: Cryo-EM structure, enzymatic activity and genome targeting of canonical PRC1
Authors: Ciapponi M / Cafiso M / Schkoelziger S / Benda C / Bonnet J / Mueller J
History
DepositionFeb 10, 2026-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56669.png

Downloads & links

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Map

FileDownload / File: emd_56669.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.85 Å/pix.
x 400 pix.
= 340.48 Å		0.85 Å/pix.
x 400 pix.
= 340.48 Å		0.85 Å/pix.
x 400 pix.
= 340.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8512 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.2812143 - 0.647978
Average (Standard dev.)0.00044160284 (±0.016586456)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 340.47998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_56669_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Focus refinement sharpened map

Fileemd_56669_additional_1.map
AnnotationFocus refinement sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened map

Fileemd_56669_additional_2.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of unsharpened map

Fileemd_56669_half_map_1.map
AnnotationHalf map A of unsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of unsharpened map

Fileemd_56669_half_map_2.map
AnnotationHalf map B of unsharpened map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human PRC1.4 in complex with native UBCH5C bound to a H3Kc27me3 m...

EntireName: Human PRC1.4 in complex with native UBCH5C bound to a H3Kc27me3 mononucleosome
Components
  • Complex: Human PRC1.4 in complex with native UBCH5C bound to a H3Kc27me3 mononucleosome
    • Protein or peptide: Isoform 2 of Polyhomeotic-like protein 2
    • Protein or peptide: Chromobox 7
    • Protein or peptide: E3 ubiquitin-protein ligase RING2
    • Protein or peptide: Polycomb complex protein BMI-1
    • Protein or peptide: Ubiquitin-conjugating enzyme E2 D3
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
    • DNA: DNA (151-MER)
    • DNA: DNA (151-MER)
  • Ligand: ZINC ION

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Supramolecule #1: Human PRC1.4 in complex with native UBCH5C bound to a H3Kc27me3 m...

SupramoleculeName: Human PRC1.4 in complex with native UBCH5C bound to a H3Kc27me3 mononucleosome
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Isoform 2 of Polyhomeotic-like protein 2

MacromoleculeName: Isoform 2 of Polyhomeotic-like protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.200988 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GPDSMTSGNG NSASSIAGTA PQNGENKPPQ AIVKPQILTH VIEGFVIQEG AEPFPVGRSS LLVGNLKKKY AQGFLPEKLP QQDHTTTTD SEMEEPYLQE SKEEGAPLKL KCELCGRVDF AYKFKRSKRF CSMACAKRYN VGCTKRVGLF HSDRSKLQKA G AATHNRRR ...String:
GPDSMTSGNG NSASSIAGTA PQNGENKPPQ AIVKPQILTH VIEGFVIQEG AEPFPVGRSS LLVGNLKKKY AQGFLPEKLP QQDHTTTTD SEMEEPYLQE SKEEGAPLKL KCELCGRVDF AYKFKRSKRF CSMACAKRYN VGCTKRVGLF HSDRSKLQKA G AATHNRRR ASKASLPPLT KDTKKQPTGT VPLSVTAALQ LTHSQEDSSR CSDNSSYEEP LSPISASSST SRRRQGQRDL EL PDMHMRD LVGMGHHFLP SEPTKWNVED VYEFIRSLPG CQEIAEEFRA QEIDGQALLL LKEDHLMSAM NIKEGPAEKI YAR ISMLKD S

UniProtKB: Polyhomeotic-like protein 2

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Macromolecule #2: Chromobox 7

MacromoleculeName: Chromobox 7 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.268504 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
GPDSMELSAI GEQVFAVESI RKKRVRKGKV EYLVKWKGWP PKYSTWEPEE HILDPRLVMA YEEKEERDRA SGYRKRGPKP KRLLLQEPP APDVLQAAGE WEPAAQPPEE EADADLAEGP PPWTPALPSS EVTVTDITAN SITVTFREAQ AAEGFFRDRS G KF

UniProtKB: Chromobox 7

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Macromolecule #3: E3 ubiquitin-protein ligase RING2

MacromoleculeName: E3 ubiquitin-protein ligase RING2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.062707 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GPDSMSQAVQ TNGTQPLSKT WELSLYELQR TPQEAITDGL EIVVSPRSLH SELMCPICLD MLKNTMTTKE CLHRFCADCI ITALRSGNK ECPTCRKKLV SKRSLRPDPN FDALISKIYP SRDEYEAHQE RVLARINKHN NQQALSHSIE EGLKIQAMNR L QRGKKQQI ...String:
GPDSMSQAVQ TNGTQPLSKT WELSLYELQR TPQEAITDGL EIVVSPRSLH SELMCPICLD MLKNTMTTKE CLHRFCADCI ITALRSGNK ECPTCRKKLV SKRSLRPDPN FDALISKIYP SRDEYEAHQE RVLARINKHN NQQALSHSIE EGLKIQAMNR L QRGKKQQI ENGSGAEDNG DSSHCSNAST HSNQEAGPSN KRTKTSDDSG LELDNNNAAM AIDPVMDGAS EIELVFRPHP TL MEKDDSA QTRYIKTSGN ATVDHLSKYL AVRLALEELR SKGESNQMNL DTASEKQYTI YIATASGQFT VLNGSFSLEL VSE KYWKVN KPMELYYAPT KEHK

UniProtKB: E3 ubiquitin-protein ligase RING2

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Macromolecule #4: Polycomb complex protein BMI-1

MacromoleculeName: Polycomb complex protein BMI-1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.02418 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MHRTTRIKIT ELNPHLMCVL CGGYFIDATT IIECLHSFCK TCIVRYLETS KYCPICDVQV HKTRPLLNIR SDKTLQDIVY KLVPGLFKN EMKRRRDFYA AHPSADAANG SNEDRGEVAD EDKRIITDDE IISLSIEFFD QNRLDRKVNK DKEKSKEEVN D KRYLRCPA ...String:
MHRTTRIKIT ELNPHLMCVL CGGYFIDATT IIECLHSFCK TCIVRYLETS KYCPICDVQV HKTRPLLNIR SDKTLQDIVY KLVPGLFKN EMKRRRDFYA AHPSADAANG SNEDRGEVAD EDKRIITDDE IISLSIEFFD QNRLDRKVNK DKEKSKEEVN D KRYLRCPA AMTVMHLRKF LRSKMDIPNT FQIDVMYEEE PLKDYYTLMD IAYIYTWRRN GPLPLKYRVR PTCKRMKISH QR DGLTNAG ELESDSGSDK ANSPAGGIPS TSSCLPSPST PVQSPHPQFP HISSTMNGTS NSPSGNHQSS FANRPRKSSV NGS SATSSG GSGSLEVLFQ

UniProtKB: Polycomb complex protein BMI-1

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Macromolecule #5: Ubiquitin-conjugating enzyme E2 D3

MacromoleculeName: Ubiquitin-conjugating enzyme E2 D3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: E2 ubiquitin-conjugating enzyme
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.706133 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MALKRINKEL SDLARDPPAQ CSAGPVGDDM FHWQATIMGP NDSPYQGGVF FLTIHFPTDY PFKPPKVAFT TRIYHPNINS NGSICLDIL RSQWSPALTI SKVLLSICSL LCDPNPDDPL VPEIARIYKT DRDKYNRISR EWTQKYAM

UniProtKB: Ubiquitin-conjugating enzyme E2 D3

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Macromolecule #6: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus (frog)
Molecular weightTheoretical: 15.271863 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEASEAY LVALFEDTNL AAIHAKRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3

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Macromolecule #7: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus (frog)
Molecular weightTheoretical: 11.263231 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG

UniProtKB: Histone H4

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Macromolecule #8: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus (frog)
Molecular weightTheoretical: 13.978241 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKQGGKT RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAVRN DEELNKLLGR VTIAQGGVLP NIQSVLLPKK TESSKSAKSK

UniProtKB: Histone H2A

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Macromolecule #9: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus (frog)
Molecular weightTheoretical: 13.524752 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AKSAPAPKKG SKKAVTKTQK KDGKKRRKTR KESYAIYVYK VLKQVHPDTG ISSKAMSIMN SFVNDVFERI AGEASRLAHY NKRSTITSR EIQTAVRLLL PGELAKHAVS EGTKAVTKYT SAK

UniProtKB: Histone H2B

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Macromolecule #10: DNA (151-MER)

MacromoleculeName: DNA (151-MER) / type: dna / ID: 10 / 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 #11: DNA (151-MER)

MacromoleculeName: DNA (151-MER) / type: dna / ID: 11 / 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 #12: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 12 / Number of copies: 4 / 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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.45 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: Ab intio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 304443
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
ChainPDB ID
source_name: AlphaFold, initial_model_type: in silico model
source_name: PDB, initial_model_type: experimental model

4r8p

Output model

PDB-28oe:
Human PRC1.4 in complex with native UBCH5C bound to a H3Kc27me3 mononucleosome

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  • 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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