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Yorodumi- EMDB-34588: Cryo-EM structure of the p300 catalytic core bound to the H4K12ac... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34588 | |||||||||
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Title | Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 1 (3.2 angstrom resolution) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Acetyl taransferase / Complex / Nucleosome / TRANSFERASE / TRANSFERASE-DNA complex | |||||||||
Function / homology | Function and homology information behavioral defense response / peptidyl-lysine propionylation / histone lactyltransferase (CoA-dependent) activity / peptidyl-lysine crotonylation / peptidyl-lysine butyrylation / histone butyryltransferase activity / histone H3K122 acetyltransferase activity / swimming / peptide butyryltransferase activity / histone H2B acetyltransferase activity ...behavioral defense response / peptidyl-lysine propionylation / histone lactyltransferase (CoA-dependent) 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 / protein propionyltransferase activity / NOTCH2 intracellular domain regulates transcription / peptidyl-lysine acetylation / macrophage derived foam cell differentiation / lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / STAT family protein binding / histone H4 acetyltransferase activity / cellular response to L-leucine / internal peptidyl-lysine acetylation / histone H3 acetyltransferase activity / NFE2L2 regulating ER-stress associated genes / peptide N-acetyltransferase activity / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / acetylation-dependent protein binding / NGF-stimulated transcription / STAT3 nuclear events downstream of ALK signaling / histone H3K18 acetyltransferase activity / Polo-like kinase mediated events / 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 / NFE2L2 regulating MDR associated enzymes / regulation of androgen receptor signaling pathway / positive regulation of T-helper 17 cell lineage commitment / regulation of mitochondrion organization / positive regulation by host of viral transcription / face morphogenesis / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / Regulation of FOXO transcriptional activity by acetylation / RUNX3 regulates NOTCH signaling / Regulation of gene expression by Hypoxia-inducible Factor / regulation of glycolytic process / Nuclear events mediated by NFE2L2 / NOTCH4 Intracellular Domain Regulates Transcription / Regulation of NFE2L2 gene expression / NOTCH3 Intracellular Domain Regulates Transcription / platelet formation / NFE2L2 regulating anti-oxidant/detoxification enzymes / TRAF6 mediated IRF7 activation / NFE2L2 regulating tumorigenic genes / megakaryocyte development / peptide-lysine-N-acetyltransferase activity / FOXO-mediated transcription of cell death genes / regulation of tubulin deacetylation / nuclear androgen receptor binding / acyltransferase activity / internal protein amino acid acetylation / protein acetylation / fat cell differentiation / positive regulation of transforming growth factor beta receptor signaling pathway / Formation of paraxial mesoderm / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / PI5P Regulates TP53 Acetylation / acetyltransferase activity / stimulatory C-type lectin receptor signaling pathway / Zygotic genome activation (ZGA) / protein localization to CENP-A containing chromatin / RUNX3 regulates p14-ARF / CENP-A containing nucleosome / NF-kappaB binding / histone acetyltransferase complex / negative regulation of tumor necrosis factor-mediated signaling pathway / Replacement of protamines by nucleosomes in the male pronucleus / Attenuation phase / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Packaging Of Telomere Ends / cellular response to nutrient levels / negative regulation of protein-containing complex assembly / negative regulation of gluconeogenesis / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / telomere organization / Chromatin modifying enzymes / somitogenesis / canonical NF-kappaB signal transduction / Deposition of new CENPA-containing nucleosomes at the centromere / pre-mRNA intronic binding / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / regulation of cellular response to heat / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / histone acetyltransferase activity / skeletal muscle tissue development / Meiotic synapsis / histone acetyltransferase Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Kikuchi M / Morita S / Wakamori M / Shin S / Uchikubo-Kamo T / Shirouzu M / Umehara T | |||||||||
Funding support | Japan, 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Epigenetic mechanisms to propagate histone acetylation by p300/CBP. Authors: Masaki Kikuchi / Satoshi Morita / Masatoshi Wakamori / Shin Sato / Tomomi Uchikubo-Kamo / Takehiro Suzuki / Naoshi Dohmae / Mikako Shirouzu / Takashi Umehara / Abstract: Histone acetylation is important for the activation of gene transcription but little is known about its direct read/write mechanisms. Here, we report cryogenic electron microscopy structures in which ...Histone acetylation is important for the activation of gene transcription but little is known about its direct read/write mechanisms. Here, we report cryogenic electron microscopy structures in which a p300/CREB-binding protein (CBP) multidomain monomer recognizes histone H4 N-terminal tail (NT) acetylation (ac) in a nucleosome and acetylates non-H4 histone NTs within the same nucleosome. p300/CBP not only recognized H4NTac via the bromodomain pocket responsible for reading, but also interacted with the DNA minor grooves via the outside of that pocket. This directed the catalytic center of p300/CBP to one of the non-H4 histone NTs. The primary target that p300 writes by reading H4NTac was H2BNT, and H2BNTac promoted H2A-H2B dissociation from the nucleosome. We propose a model in which p300/CBP replicates histone N-terminal tail acetylation within the H3-H4 tetramer to inherit epigenetic storage, and transcribes it from the H3-H4 tetramer to the H2B-H2A dimers to activate context-dependent gene transcription through local nucleosome destabilization. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34588.map.gz | 140.2 MB | EMDB map data format | |
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Header (meta data) | emd-34588-v30.xml emd-34588.xml | 20.1 KB 20.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_34588_fsc.xml | 12 KB | Display | FSC data file |
Images | emd_34588.png | 82.8 KB | ||
Masks | emd_34588_msk_1.map | 149.9 MB | Mask map | |
Others | emd_34588_half_map_1.map.gz emd_34588_half_map_2.map.gz | 118.4 MB 118.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34588 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34588 | HTTPS FTP |
-Related structure data
Related structure data | 8hagMC 8hahC 8haiC 8hajC 8hakC 8halC 8hamC 8hanC 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_34588.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.829 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_34588_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34588_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34588_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : the p300 catalytic core bound to the H4K12acK16ac nucleosome
Entire | Name: the p300 catalytic core bound to the H4K12acK16ac nucleosome |
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Components |
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-Supramolecule #1: the p300 catalytic core bound to the H4K12acK16ac nucleosome
Supramolecule | Name: the p300 catalytic core bound to the H4K12acK16ac nucleosome type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: p300 was expressed in insect cells. |
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Source (natural) | Organism: Homo sapiens (human) |
-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 UniProtKB: Histone H3.1 |
-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: 11.345289 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SGRGKGGKGL G(ALY)GGA(ALY)RHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TY TEHAKRK TVTAMDVVYA LKRQGRTLYG FGG |
-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: 14.034355 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SGRGKQGGKA RAKAKTRSSR AGLQFPVGRV HRLLRKGNYS ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAIRN DEELNKLLGR VTIAQGGVLP NIQAVLLPKK TESHHKAKGK UniProtKB: Histone H2A type 1-B/E |
-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: 13.935239 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSI YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSAK UniProtKB: Histone H2B type 1-J |
-Macromolecule #5: Histone acetyltransferase p300
Macromolecule | Name: Histone acetyltransferase p300 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: histone acetyltransferase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 92.314391 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: GSSGSSGIFK PEELRQALMP TLEALYRQDP ESLPFRQPVD PQLLGIPDYF DIVKSPMDLS TIKRKLDTGQ YQEPWQYVDD IWLMFNNAW LYNRKTSRVY KYCSKLSEVF EQEIDPVMQS LGYCCGRKLE FSPQTLCCYG KQLCTIPRDA TYYSYQNRYH F CEKCFNEI ...String: GSSGSSGIFK PEELRQALMP TLEALYRQDP ESLPFRQPVD PQLLGIPDYF DIVKSPMDLS TIKRKLDTGQ YQEPWQYVDD IWLMFNNAW LYNRKTSRVY KYCSKLSEVF EQEIDPVMQS LGYCCGRKLE FSPQTLCCYG KQLCTIPRDA TYYSYQNRYH F CEKCFNEI QGESVSLGDD PSQPQTTINK EQFSKRKNDT LDPELFVECT ECGRKMHQIC VLHHEIIWPA GFVCDGCLKK SA RTRKENK FSAKRLPSTR LGTFLENRVN DFLRRQNHPE SGEVTVRVVH ASDKTVEVKP GMKARFVDSG EMAESFPYRT KAL FAFEEI DGVDLCFFGM HVQEYGSDCP PPNQRRVYIS YLDSVHFFRP KCLRTAVYHE ILIGYLEYVK KLGYTTGHIW ACPP SEGDD YIFHCHPPDQ KIPKPKRLQE WYKKMLDKAV SERIVHDYKD IFKQATEDRL TSAKELPYFE GDFWPNVLEE SIKEL EQEE EERKREENTS NESTDVTKGD SKNAKKKNNK KTSKNKSSLS RGNKKKPGMP NVSNDLSQKL YATMEKHKEV FFVIRL IAG PAANSLPPIV DPDPLIPCDL MDGRDAFLTL ARDKHLEFSS LRRAQWSTMC MLVELHTQSQ DRFVYTCNEC KHHVETR WH CTVCEDYDLC ITCYNTKNHD HKMEKLGLGL DDESNNQQAA ATQSPGDSRR LSIQRCIQSL VHACQCRNAN CSLPSCQK M KRVVQHTKGC KRKTNGGCPI CKQLIALCCY HAKHCQENKC PVPFCLNIKQ KLRQQQLQHR LQQAQMLRRR MASMQ UniProtKB: Histone acetyltransferase p300 |
-Macromolecule #6: DNA (180-mer)
Macromolecule | Name: DNA (180-mer) / type: dna / ID: 6 / Number of copies: 2 / Classification: DNA |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 55.560527 KDa |
Sequence | String: (DA)(DT)(DC)(DC)(DG)(DT)(DC)(DC)(DG)(DT) (DT)(DA)(DC)(DC)(DG)(DC)(DC)(DA)(DT)(DC) (DA)(DA)(DT)(DA)(DT)(DC)(DC)(DA)(DC) (DC)(DT)(DG)(DC)(DA)(DG)(DA)(DT)(DT)(DC) (DT) (DA)(DC)(DC)(DA)(DA)(DA) ...String: (DA)(DT)(DC)(DC)(DG)(DT)(DC)(DC)(DG)(DT) (DT)(DA)(DC)(DC)(DG)(DC)(DC)(DA)(DT)(DC) (DA)(DA)(DT)(DA)(DT)(DC)(DC)(DA)(DC) (DC)(DT)(DG)(DC)(DA)(DG)(DA)(DT)(DT)(DC) (DT) (DA)(DC)(DC)(DA)(DA)(DA)(DA)(DG) (DT)(DG)(DT)(DA)(DT)(DT)(DT)(DG)(DG)(DA) (DA)(DA) (DC)(DT)(DG)(DC)(DT)(DC)(DC) (DA)(DT)(DC)(DA)(DA)(DA)(DA)(DG)(DG)(DC) (DA)(DT)(DG) (DT)(DT)(DC)(DA)(DG)(DC) (DT)(DG)(DA)(DA)(DT)(DT)(DC)(DA)(DG)(DC) (DT)(DG)(DA)(DA) (DC)(DA)(DT)(DG)(DC) (DC)(DT)(DT)(DT)(DT)(DG)(DA)(DT)(DG)(DG) (DA)(DG)(DC)(DA)(DG) (DT)(DT)(DT)(DC) (DC)(DA)(DA)(DA)(DT)(DA)(DC)(DA)(DC)(DT) (DT)(DT)(DT)(DG)(DG)(DT) (DA)(DG)(DA) (DA)(DT)(DC)(DT)(DG)(DC)(DA)(DG)(DG)(DT) (DG)(DG)(DA)(DT)(DA)(DT)(DT) (DG)(DA) (DT)(DG)(DG)(DC)(DG)(DG)(DT)(DA)(DA)(DC) (DG)(DG)(DA)(DC)(DG)(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: 7.2 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k 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: 2.0 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |