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- EMDB-34594: Cryo-EM structure of the p300 catalytic core bound to the H4K12ac... -
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Open data
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Basic information
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Title | Cryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 4 (4.5 angstrom resolution) | |||||||||
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![]() | Acetyl taransferase / ![]() ![]() ![]() | |||||||||
Function / homology | ![]() 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 / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Kikuchi M / Morita S / Wakamori M / Shin S / Uchikubo-Kamo T / Shirouzu M / Umehara T | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 55.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20 KB 20 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.9 KB | Display | ![]() |
Images | ![]() | 74.6 KB | ||
Masks | ![]() | 59.6 MB | ![]() | |
Others | ![]() ![]() | 46.2 MB 46.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8hakMC ![]() 8hagC ![]() 8hahC ![]() 8haiC ![]() 8hajC ![]() 8halC ![]() 8hamC ![]() 8hanC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.47 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Half map: #2
File | emd_34594_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_34594_half_map_2.map | ||||||||||||
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Density Histograms |
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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: #1-#6 / Details: p300 was expressed in insect cells. |
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Source (natural) | Organism: ![]() ![]() |
-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: ![]() ![]() |
Molecular weight | Theoretical: 15.305969 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEACEAY LVGLFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA UniProtKB: ![]() |
-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: ![]() ![]() |
Molecular weight | Theoretical: 11.345289 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
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: ![]() ![]() |
Molecular weight | Theoretical: 14.034355 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
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: ![]() ![]() |
Molecular weight | Theoretical: 13.804045 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: PEPAKSAPAP KKGSKKAVTK AQKKDGKKRK RSRKESYSIY VYKVLKQVHP DTGISSKAMG IMNSFVNDIF ERIAGEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSAK UniProtKB: Histone H2B type 1-J |
-Macromolecule #6: Histone acetyltransferase p300
Macromolecule | Name: Histone acetyltransferase p300 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: ![]() |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 92.314391 KDa |
Recombinant expression | Organism: ![]() ![]() |
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 #5: DNA (180-mer)
Macromolecule | Name: DNA (180-mer) / type: dna / ID: 5 / Number of copies: 2 / Classification: DNA |
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Source (natural) | Organism: ![]() ![]() |
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 | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.2 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |