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Yorodumi- EMDB-32373: Cryo-EM structure of nucleosome in complex with p300 acetyltransf... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32373 | |||||||||||||||||||||||||||||||||||||||
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Title | Cryo-EM structure of nucleosome in complex with p300 acetyltransferase catalytic core (complex I) | |||||||||||||||||||||||||||||||||||||||
Map data | The cryo-EM map of p300-NCP complex I | |||||||||||||||||||||||||||||||||||||||
Sample |
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Function / homology | Function and homology information behavioral defense response / protein propionyltransferase activity / peptidyl-lysine propionylation / histone lactyltransferase activity / peptidyl-lysine crotonylation / peptidyl-lysine butyrylation / histone butyryltransferase activity / histone H3K122 acetyltransferase activity / swimming / peptide butyryltransferase activity ...behavioral defense response / protein propionyltransferase activity / peptidyl-lysine propionylation / histone lactyltransferase activity / peptidyl-lysine crotonylation / peptidyl-lysine butyrylation / histone butyryltransferase activity / histone H3K122 acetyltransferase activity / swimming / peptide butyryltransferase activity / histone H2B acetyltransferase activity / thigmotaxis / peptide 2-hydroxyisobutyryltransferase activity / histone crotonyltransferase activity / NOTCH2 intracellular domain regulates transcription / lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / peptidyl-lysine acetylation / histone H4 acetyltransferase activity / histone H3 acetyltransferase activity / cellular response to L-leucine / internal peptidyl-lysine acetylation / NFE2L2 regulating ER-stress associated genes / peptide N-acetyltransferase activity / STAT3 nuclear events downstream of ALK signaling / acetylation-dependent protein binding / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / NGF-stimulated transcription / Polo-like kinase mediated events / histone H3K18 acetyltransferase activity / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity / NFE2L2 regulates pentose phosphate pathway genes / regulation of androgen receptor signaling pathway / NFE2L2 regulating MDR associated enzymes / positive regulation by host of viral transcription / regulation of mitochondrion organization / face morphogenesis / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / NOTCH4 Intracellular Domain Regulates Transcription / Regulation of FOXO transcriptional activity by acetylation / Regulation of gene expression by Hypoxia-inducible Factor / Nuclear events mediated by NFE2L2 / Regulation of NFE2L2 gene expression / NOTCH3 Intracellular Domain Regulates Transcription / regulation of glycolytic process / platelet formation / nuclear androgen receptor binding / NFE2L2 regulating anti-oxidant/detoxification enzymes / megakaryocyte development / TRAF6 mediated IRF7 activation / regulation of tubulin deacetylation / macrophage derived foam cell differentiation / peptide-lysine-N-acetyltransferase activity / FOXO-mediated transcription of cell death genes / NFE2L2 regulating tumorigenic genes / internal protein amino acid acetylation / STAT family protein binding / acyltransferase activity / fat cell differentiation / protein acetylation / Formation of paraxial mesoderm / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / positive regulation of transforming growth factor beta receptor signaling pathway / PI5P Regulates TP53 Acetylation / Zygotic genome activation (ZGA) / stimulatory C-type lectin receptor signaling pathway / acetyltransferase activity / cellular response to nutrient levels / RUNX3 regulates p14-ARF / NF-kappaB binding / histone acetyltransferase complex / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / negative regulation of tumor necrosis factor-mediated signaling pathway / canonical NF-kappaB signal transduction / Attenuation phase / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / negative regulation of protein-containing complex assembly / negative regulation of gluconeogenesis / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / somitogenesis / epigenetic regulation of gene expression / pre-mRNA intronic binding / Packaging Of Telomere Ends / regulation of cellular response to heat / skeletal muscle tissue development / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / histone acetyltransferase activity / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / transcription initiation-coupled chromatin remodeling Similarity search - Function | |||||||||||||||||||||||||||||||||||||||
Biological species | Homo sapiens (human) / synthetic construct (others) | |||||||||||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.95 Å | |||||||||||||||||||||||||||||||||||||||
Authors | Hatazawa S / Liu J / Takizawa Y / Zandian M / Negishi L / Kutateladze TG / Kurumizaka H | |||||||||||||||||||||||||||||||||||||||
Funding support | Japan, United States, 12 items
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Citation | Journal: iScience / Year: 2022 Title: Structural basis for binding diversity of acetyltransferase p300 to the nucleosome. Authors: Suguru Hatazawa / Jiuyang Liu / Yoshimasa Takizawa / Mohamad Zandian / Lumi Negishi / Tatiana G Kutateladze / Hitoshi Kurumizaka / Abstract: p300 is a human acetyltransferase that associates with chromatin and mediates vital cellular processes. We now report the cryo-electron microscopy structures of the p300 catalytic core in complex ...p300 is a human acetyltransferase that associates with chromatin and mediates vital cellular processes. We now report the cryo-electron microscopy structures of the p300 catalytic core in complex with the nucleosome core particle (NCP). In the most resolved structure, the HAT domain and bromodomain of p300 contact nucleosomal DNA at superhelical locations 2 and 3, and the catalytic site of the HAT domain are positioned near the N-terminal tail of histone H4. Mutations of the p300-DNA interfacial residues of p300 substantially decrease binding to NCP. Three additional classes of p300-NCP complexes show different modes of the p300-NCP complex formation. Our data provide structural details critical to our understanding of the mechanism by which p300 acetylates multiple sites on the nucleosome. | |||||||||||||||||||||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32373.map.gz | 5.1 MB | EMDB map data format | |
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Header (meta data) | emd-32373-v30.xml emd-32373.xml | 19.6 KB 19.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_32373_fsc.xml | 8.6 KB | Display | FSC data file |
Images | emd_32373.png | 83.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32373 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32373 | HTTPS FTP |
-Related structure data
Related structure data | 7w9vMC 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_32373.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | The cryo-EM map of p300-NCP complex I | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Nucleosome in complex with p300 acetyltransferase catalytic core ...
Entire | Name: Nucleosome in complex with p300 acetyltransferase catalytic core (complex I) |
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Components |
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-Supramolecule #1: Nucleosome in complex with p300 acetyltransferase catalytic core ...
Supramolecule | Name: Nucleosome in complex with p300 acetyltransferase catalytic core (complex I) type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: Histone H3.1
Macromolecule | Name: Histone H3.1 / 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: 15.305969 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEACEAY LVGLFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA |
-Macromolecule #2: Histone H4
Macromolecule | Name: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 11.676703 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GSHMSGRGKG GKGLGKGGAK RHRKVLRDNI QGITKPAIRR LARRGGVKRI SGLIYEETRG VLKVFLENVI RDAVTYTEHA KRKTVTAMD VVYALKRQGR TLYGFGG |
-Macromolecule #3: Histone H2A type 1-B/E
Macromolecule | Name: Histone H2A type 1-B/E / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 14.447825 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GSHMSGRGKQ GGKARAKAKT RSSRAGLQFP VGRVHRLLRK GNYSERVGAG APVYLAAVLE YLTAEILELA GNAARDNKKT RIIPRHLQL AIRNDEELNK LLGRVTIAQG GVLPNIQAVL LPKKTESHHK AKGK |
-Macromolecule #4: Histone H2B type 1-J
Macromolecule | Name: Histone H2B type 1-J / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 14.217516 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GSHMPEPAKS APAPKKGSKK AVTKAQKKDG KKRKRSRKES YSIYVYKVLK QVHPDTGISS KAMGIMNSFV NDIFERIAGE ASRLAHYNK RSTITSREIQ TAVRLLLPGE LAKHAVSEGT KAVTKYTSAK |
-Macromolecule #7: Histone acetyltransferase p300
Macromolecule | Name: Histone acetyltransferase p300 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: histone acetyltransferase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 74.42657 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: TQSSPAPGQS KKKIFKPEEL RQALMPTLEA LYRQDPESLP FRQPVDPQLL GIPDYFDIVK SPMDLSTIKR KLDTGQYQEP WQYVDDIWL MFNNAWLYNR KTSRVYKYCS KLSEVFEQEI DPVMQSLGYC CGRKLEFSPQ TLCCYGKQLC TIPRDATYYS Y QNRYHFCE ...String: TQSSPAPGQS KKKIFKPEEL RQALMPTLEA LYRQDPESLP FRQPVDPQLL GIPDYFDIVK SPMDLSTIKR KLDTGQYQEP WQYVDDIWL MFNNAWLYNR KTSRVYKYCS KLSEVFEQEI DPVMQSLGYC CGRKLEFSPQ TLCCYGKQLC TIPRDATYYS Y QNRYHFCE KCFNEIQGES VSLGDDPSQP QTTINKEQFS KRKNDTLDPE LFVECTECGR KMHQICVLHH EIIWPAGFVC DG CLKKSAR TRKENKFSAK RLPSTRLGTF LENRVNDFLR RQNHPESGEV TVRVVHASDK TVEVKPGMKA RFVDSGEMAE SFP YRTKAL FAFEEIDGVD LCFFGMHVQE YGSDCPPPNQ RRVYISYLDS VHFFRPKCLR TAVYHEILIG YLEYVKKLGY TTGH IWACP PSEGDDYIFH CHPPDQKIPK PKRLQEWFKK MLDKAVSERI VHDYKDIFKQ ATEDRLTSAK ELPYFEGDFW PNVLE ESIK ESGGSGSQKL YATMEKHKEV FFVIRLIAGP AANSLPPIVD PDPLIPCDLM DGRDAFLTLA RDKHLEFSSL RRAQWS TMC MLVELHTQSQ DRFVYTCNEC KHHVETRWHC TVCEDYDLCI TCYNTKNHDH KMEKLGLGLD DESNNQQHHH HHHHH |
-Macromolecule #5: DNA (145-MER)
Macromolecule | Name: DNA (145-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 44.520383 KDa |
Sequence | String: (DA)(DT)(DC)(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) ...String: (DA)(DT)(DC)(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)(DG) (DA)(DT) |
-Macromolecule #6: DNA (145-MER)
Macromolecule | Name: DNA (145-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 44.99166 KDa |
Sequence | String: (DA)(DT)(DC)(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: (DA)(DT)(DC)(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)(DG) (DA)(DT) |
-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: 2.3000000000000003 µm / Nominal defocus min: 1.2 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 56.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |