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Yorodumi- EMDB-41922: Cryo-EM structure of human DNMT3A UDR bound to H2AK119ub1-modifie... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41922 | |||||||||
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Title | Cryo-EM structure of human DNMT3A UDR bound to H2AK119ub1-modified nucleosome | |||||||||
Map data | main map | |||||||||
Sample |
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Keywords | DNA cytosine methyltransferase / STRUCTURAL PROTEIN-TRANSFERASE-DNA complex | |||||||||
Function / homology | Function and homology information positive regulation of cellular response to hypoxia / regulatory ncRNA-mediated heterochromatin formation / cellular response to bisphenol A / protein-cysteine methyltransferase activity / unmethylated CpG binding / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting / S-adenosylmethionine metabolic process / SUMOylation of DNA methylation proteins ...positive regulation of cellular response to hypoxia / regulatory ncRNA-mediated heterochromatin formation / cellular response to bisphenol A / protein-cysteine methyltransferase activity / unmethylated CpG binding / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting / S-adenosylmethionine metabolic process / SUMOylation of DNA methylation proteins / XY body / cellular response to ethanol / response to vitamin A / DNA methylation-dependent constitutive heterochromatin formation / lncRNA binding / negative regulation of gene expression via chromosomal CpG island methylation / response to ionizing radiation / hepatocyte apoptotic process / catalytic complex / chromosome, centromeric region / heterochromatin / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / FLT3 signaling by CBL mutants / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Prevention of phagosomal-lysosomal fusion / Glycogen synthesis / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / TICAM1,TRAF6-dependent induction of TAK1 complex / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of FZD by ubiquitination / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / p75NTR recruits signalling complexes / APC/C:Cdc20 mediated degradation of Cyclin B / VLDLR internalisation and degradation / Downregulation of ERBB4 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of PTEN localization / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / DNA methylation / Translesion synthesis by POLK / Transferases; Transferring one-carbon groups; Methyltransferases / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / InlB-mediated entry of Listeria monocytogenes into host cell / PINK1-PRKN Mediated Mitophagy / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / PRC2 methylates histones and DNA / response to cocaine / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Defective pyroptosis / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / activated TAK1 mediates p38 MAPK activation / TNFR2 non-canonical NF-kB pathway / Regulation of signaling by CBL / Vpu mediated degradation of CD4 / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Xenopus laevis (African clawed frog) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.23 Å | |||||||||
Authors | Chen X / Song J | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: Cryo-EM structure of human DNMT3A N-terminal domain bound to H2AK119Ub nucleosome Authors: Chen X / Song J | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41922.map.gz | 25.1 MB | EMDB map data format | |
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Header (meta data) | emd-41922-v30.xml emd-41922.xml | 19.5 KB 19.5 KB | Display Display | EMDB header |
Images | emd_41922.png | 102.3 KB | ||
Filedesc metadata | emd-41922.cif.gz | 6.2 KB | ||
Others | emd_41922_additional_1.map.gz | 12.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41922 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41922 | HTTPS FTP |
-Validation report
Summary document | emd_41922_validation.pdf.gz | 511.6 KB | Display | EMDB validaton report |
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Full document | emd_41922_full_validation.pdf.gz | 511.1 KB | Display | |
Data in XML | emd_41922_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | emd_41922_validation.cif.gz | 7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41922 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41922 | HTTPS FTP |
-Related structure data
Related structure data | 8u5hMC C: citing same article (ref.) M: atomic model generated by this map |
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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_41922.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | main map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.2347 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: additional map
File | emd_41922_additional_1.map | ||||||||||||
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Annotation | additional map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : DNMT3A N-terminal domain and H2AK119Ub nucleosome complex
Entire | Name: DNMT3A N-terminal domain and H2AK119Ub nucleosome complex |
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Components |
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-Supramolecule #1: DNMT3A N-terminal domain and H2AK119Ub nucleosome complex
Supramolecule | Name: DNMT3A N-terminal domain and H2AK119Ub nucleosome complex type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: DNA (cytosine-5)-methyltransferase 3A
Macromolecule | Name: DNA (cytosine-5)-methyltransferase 3A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 11.070631 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: PEASRAVENG CCTPKEGRGA PAEAGKEQKE TNIESMKMEG SRGRLRGGLG WESSLRQRPM PRLTFQAGDP YYISKRKRDE WLARWKREA EKKAKVIAG UniProtKB: DNA (cytosine-5)-methyltransferase 3A |
-Macromolecule #3: Ubiquitin
Macromolecule | Name: Ubiquitin / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 8.576831 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG UniProtKB: Polyubiquitin-C |
-Macromolecule #5: Histone H3.3C
Macromolecule | Name: Histone H3.3C / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Molecular weight | Theoretical: 15.521349 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MARTKQTARK STGGKAPRKQ LVTKAAKKCA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQRSA VMALQEASEA YLVALFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA UniProtKB: Histone H3.3C |
-Macromolecule #6: Histone H4
Macromolecule | Name: Histone H4 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Molecular weight | Theoretical: 11.394426 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG UniProtKB: Histone H4 |
-Macromolecule #7: Histone H2A
Macromolecule | Name: Histone H2A / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Molecular weight | Theoretical: 14.083398 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MSGRGKQGGK TRAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAVR NDEELNKLLG RVTIAQGGVL PNIQSVLLPK CTESSKSAKS K UniProtKB: Histone H2A |
-Macromolecule #8: Histone H2B 1.1
Macromolecule | Name: Histone H2B 1.1 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Molecular weight | Theoretical: 13.655948 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MAKSAPAPKK GSKKAVTKTQ KKDGKKRRKT RKESYAIYVY KVLKQVHPDT GISSKAMSIM NSFVNDVFER IAGEASRLAH YNKRSTITS REIQTAVRLL LPGELAKHAV SEGTKAVTKY TSAK UniProtKB: Histone H2B 1.1 |
-Macromolecule #2: nucleosome DNA
Macromolecule | Name: nucleosome DNA / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 55.176137 KDa |
Sequence | String: (DG)(DC)(DT)(DC)(DT)(DC)(DT)(DA)(DC)(DG) (DT)(DA)(DA)(DA)(DC)(DA)(DT)(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) ...String: (DG)(DC)(DT)(DC)(DT)(DC)(DT)(DA)(DC)(DG) (DT)(DA)(DA)(DA)(DC)(DA)(DT)(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)(DA)(DC)(DT)(DT)(DA)(DC) (DC)(DC)(DA)(DC)(DT)(DT)(DC)(DG) |
-Macromolecule #4: nucleosome DNA
Macromolecule | Name: nucleosome DNA / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 55.963656 KDa |
Sequence | String: (DC)(DG)(DA)(DA)(DG)(DT)(DG)(DG)(DG)(DT) (DA)(DA)(DG)(DT)(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) ...String: (DC)(DG)(DA)(DA)(DG)(DT)(DG)(DG)(DG)(DT) (DA)(DA)(DG)(DT)(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) (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)(DA)(DT)(DG)(DT)(DT)(DT)(DA)(DC)(DG) (DT)(DA)(DG)(DA)(DG)(DA)(DG)(DC) |
-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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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 86685 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |