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- EMDB-34207: Cryo-EM structure of PRC1 bound to H2AK119-UbcH5b-Ub nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-34207
TitleCryo-EM structure of PRC1 bound to H2AK119-UbcH5b-Ub nucleosome
Map data
Sample
  • Complex: Complex of PRC1 and H2AK119-UbcH5b-Ub nucleosome
    • Protein or peptide: x 9 types
    • DNA: x 2 types
  • Ligand: x 1 types
KeywordsPRC1 / Ring1B / Bmi1 / H2AK119 / H2AK119-UbcH5c-Ub / Nucleosome / NUCLEAR PROTEIN
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 / hypothalamus gonadotrophin-releasing hormone neuron development / anterior/posterior axis specification ...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 / hypothalamus gonadotrophin-releasing hormone neuron development / anterior/posterior axis specification / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / female gonad development / seminiferous tubule development / negative regulation of gene expression, epigenetic / Transcriptional Regulation by E2F6 / germ cell development / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / male meiosis I / MLL1 complex / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / ubiquitin ligase complex / : / SUMOylation of DNA damage response and repair proteins / energy homeostasis / protein localization to CENP-A containing chromatin / regulation of neuron apoptotic process / neuron projection morphogenesis / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / regulation of proteasomal protein catabolic process / Packaging Of Telomere Ends / Maturation of protein E / Maturation of protein E / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / 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 / Deposition of new CENPA-containing nucleosomes at the centromere / 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 / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / APC/C:Cdc20 mediated degradation of Cyclin B / SUMOylation of transcription cofactors / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / RNA Polymerase I Promoter Opening / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / epigenetic regulation of gene expression / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Inhibition of DNA recombination at telomere / Regulation of innate immune responses to cytosolic DNA / Pexophagy / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Assembly of the ORC complex at the origin of replication / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Meiotic synapsis / VLDLR internalisation and degradation / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / DNA methylation / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / Regulation of PTEN gene transcription / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / positive regulation of protein ubiquitination / Condensation of Prophase Chromosomes / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Chromatin modifications during the maternal to zygotic transition (MZT)
Similarity search - Function
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, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / : / Histone H2B signature. ...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, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A 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 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Ubiquitin domain / Histone-fold / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Histone H4 / Histone H3 / Histone H2B type 1-K / Histone H2A type 1-B/E / Polyubiquitin-B / Polycomb complex protein BMI-1 / E3 ubiquitin-protein ligase RING2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsAi HS / Zebin T / Zhihend D / Jiakun T / Liying Z / Jia-Bin L / Man P / Liu L
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22137005, 81621002, 21977090 China
CitationJournal: Chem / Year: 2023
Title: Synthetic E2-Ub-nucleosome conjugates for studying nucleosome ubiquitination.
Authors: Ai HS / Tong Z / Deng Z / Tian J / Zhang L / Sun M / Du Y / Xu Z / Shi Q / Liang L / Zheng Q / Li JB / Pan M / Liu L
History
DepositionSep 2, 2022-
Header (metadata) releaseApr 12, 2023-
Map releaseApr 12, 2023-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34207.png

Downloads & links

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Map

FileDownload / File: emd_34207.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 274.944 Å		1.07 Å/pix.
x 256 pix.
= 274.944 Å		1.07 Å/pix.
x 256 pix.
= 274.944 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.074 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.04757723 - 0.09762609
Average (Standard dev.)0.000117961965 (±0.0024060912)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 274.944 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_34207_msk_1.map
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Additional map: #1

Fileemd_34207_additional_1.map
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Additional map: #2

Fileemd_34207_additional_2.map
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Half map: #1

Fileemd_34207_half_map_1.map
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Half map: #2

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Sample components

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Entire : Complex of PRC1 and H2AK119-UbcH5b-Ub nucleosome

EntireName: Complex of PRC1 and H2AK119-UbcH5b-Ub nucleosome
Components
  • Complex: Complex of PRC1 and H2AK119-UbcH5b-Ub nucleosome
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-B/E
    • Protein or peptide: Histone H2B type 1-K
    • Protein or peptide: Histone H2B type 1-K
    • Protein or peptide: COMMD3 protein
    • Protein or peptide: Ring1B
    • DNA: DNA (144-MER)
    • DNA: DNA (145-MER)
    • Protein or peptide: Ubiquitin
    • Protein or peptide: UbcH5b
  • Ligand: ZINC ION

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Supramolecule #1: Complex of PRC1 and H2AK119-UbcH5b-Ub nucleosome

SupramoleculeName: Complex of PRC1 and H2AK119-UbcH5b-Ub nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 350 KDa

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Macromolecule #1: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.562577 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
KPHRYRPGTV ALREIRRYQK STELLIRKLP FQRLVREIAQ DFKTDLRFQS SAVMALQEAC EAYLVGLFED TNLCAIHAKR VTIMPKDIQ LARRIRGER

UniProtKB: Histone H3

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.704396 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
HRKVLRDNIQ GITKPAIRRL ARRGGVKRIS GLIYEETRGV LKVFLENVIR DAVTYTEHAK RKTVTAMDVV YALKRQGRTL YGFGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A type 1-B/E

MacromoleculeName: Histone H2A type 1-B/E / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.995051 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
RAKAKTRSSR AGLQFPVGRV HRLLRKGNYS ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAIRND EELNKLLGR VTIAQGGVLP NIQAVLLPKK

UniProtKB: Histone H2A type 1-B/E

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Macromolecule #4: Histone H2B type 1-K

MacromoleculeName: Histone H2B type 1-K / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.736354 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
KRSRKESYSV YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAV TKYTSAK

UniProtKB: Histone H2B type 1-K

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Macromolecule #5: Histone H2B type 1-K

MacromoleculeName: Histone H2B type 1-K / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.607174 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
RSRKESYSVY VYKVLKQVHP DTGISSKAMG IMNSFVNDIF ERIAGEASRL AHYNKRSTIT SREIQTAVRL LLPGELAKHA VSEGTKAVT KYTSAK

UniProtKB: Histone H2B type 1-K

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Macromolecule #6: COMMD3 protein

MacromoleculeName: COMMD3 protein / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.865067 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
HRTTRIKITE LNPHLMCVLC GGYFIDATTI IECLHSFCKT CIVRYLETSK YCPICDVQVH KTRPLLNIRS DKTLQDIVYK LVPGLFKNE MKRRRDFYAA HP

UniProtKB: Polycomb complex protein BMI-1

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Macromolecule #7: Ring1B

MacromoleculeName: Ring1B / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.530516 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
TWELSLYELQ RTPQEAITDG LEIVVSPRSL HSELMCPICL DMLKNTMTTK ECLHRFCADC LITALRSGNK ECPTCRKKLV SKRSLRPDP NFDALISKIY PS

UniProtKB: E3 ubiquitin-protein ligase RING2

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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: 8.576831 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

UniProtKB: Polyubiquitin-B

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Macromolecule #11: UbcH5b

MacromoleculeName: UbcH5b / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.575836 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ALKRIHKELN DLARDPPAQS SAGPVGDDMF HWQATIMGPN DSPYQGGVFF LTIHFPTDYP FKPPKVAFTT RIYHPNINSN GSICLDILR SQWSPALTIS KVLLSISSLL SDPNPDDPLV PEIARIYKTD REKYNRIARE WTQKYAM

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Macromolecule #8: DNA (144-MER)

MacromoleculeName: DNA (144-MER) / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.217172 KDa
SequenceString: (DC)(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) ...String:
(DC)(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)(DG) (DA)

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Macromolecule #9: DNA (145-MER)

MacromoleculeName: DNA (145-MER) / type: dna / ID: 9 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.992648 KDa
SequenceString: (DT)(DC)(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) ...String:
(DT)(DC)(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) (DG)(DA)

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 151276
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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