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Yorodumi- EMDB-34207: Cryo-EM structure of PRC1 bound to H2AK119-UbcH5b-Ub nucleosome -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34207 | |||||||||
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Title | Cryo-EM structure of PRC1 bound to H2AK119-UbcH5b-Ub nucleosome | |||||||||
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Sample |
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Function / homology | Function and homology information histone H2AK119 ubiquitin ligase activity / RING-like zinc finger domain binding / sex chromatin / PRC1 complex / PcG protein complex / SUMOylation of DNA methylation proteins / gastrulation with mouth forming second / SUMOylation of RNA binding proteins / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I ...histone H2AK119 ubiquitin ligase activity / RING-like zinc finger domain binding / sex chromatin / PRC1 complex / PcG protein complex / SUMOylation of DNA methylation proteins / gastrulation with mouth forming second / SUMOylation of RNA binding proteins / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / anterior/posterior axis specification / fat pad development / female gonad development / seminiferous tubule development / male meiosis I / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Transcriptional Regulation by E2F6 / germ cell development / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / MLL1 complex / heterochromatin organization / nucleosomal DNA binding / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / SUMOylation of DNA damage response and repair proteins / epigenetic regulation of gene expression / energy homeostasis / regulation of neuron apoptotic process / Packaging Of Telomere Ends / regulation of proteasomal protein catabolic process / ubiquitin ligase complex / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Maturation of protein E / Maturation of protein E / Deposition of new CENPA-containing nucleosomes at the centromere / 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 / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Inhibition of DNA recombination at telomere / Meiotic synapsis / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / InlA-mediated entry of Listeria monocytogenes into host cells / Downregulation of ERBB2:ERBB3 signaling / RNA Polymerase I Promoter Opening / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / DNA methylation / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / neuron projection morphogenesis / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Condensation of Prophase Chromosomes / SUMOylation of transcription cofactors Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.05 Å | |||||||||
Authors | Ai HS / Zebin T / Zhihend D / Jiakun T / Liying Z / Jia-Bin L / Man P / Liu L | |||||||||
Funding support | China, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34207.map.gz | 5 MB | EMDB map data format | |
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Header (meta data) | emd-34207-v30.xml emd-34207.xml | 28.5 KB 28.5 KB | Display Display | EMDB header |
Images | emd_34207.png | 73.5 KB | ||
Masks | emd_34207_msk_1.map | 64 MB | Mask map | |
Others | emd_34207_additional_1.map.gz emd_34207_additional_2.map.gz emd_34207_half_map_1.map.gz emd_34207_half_map_2.map.gz | 4.4 MB 49.6 MB 49.6 MB 49.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34207 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34207 | HTTPS FTP |
-Related structure data
Related structure data | 8grmMC 8grqC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_34207.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.074 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_34207_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_34207_additional_1.map | ||||||||||||
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Density Histograms |
-Additional map: #2
File | emd_34207_additional_2.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_34207_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_34207_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Complex of PRC1 and H2AK119-UbcH5b-Ub nucleosome
+Supramolecule #1: Complex of PRC1 and H2AK119-UbcH5b-Ub nucleosome
+Macromolecule #1: Histone H3
+Macromolecule #2: Histone H4
+Macromolecule #3: Histone H2A type 1-B/E
+Macromolecule #4: Histone H2B type 1-K
+Macromolecule #5: Histone H2B type 1-K
+Macromolecule #6: COMMD3 protein
+Macromolecule #7: Ring1B
+Macromolecule #10: Ubiquitin
+Macromolecule #11: UbcH5b
+Macromolecule #8: DNA (144-MER)
+Macromolecule #9: DNA (145-MER)
+Macromolecule #12: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
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Final angle assignment | Type: ANGULAR RECONSTITUTION |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 151276 |