[English] 日本語
Yorodumi
- EMDB-34594: Cryo-EM structure of the p300 catalytic core bound to the H4K12ac... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-34594
TitleCryo-EM structure of the p300 catalytic core bound to the H4K12acK16ac nucleosome, class 4 (4.5 angstrom resolution)
Map data
Sample
  • Complex: the p300 catalytic core bound to the H4K12acK16ac nucleosome
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-B/E
    • Protein or peptide: Histone H2B type 1-J
    • DNA: DNA (180-mer)
    • Protein or peptide: Histone acetyltransferase p300
KeywordsAcetyl 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 / lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / histone H4 acetyltransferase activity / internal peptidyl-lysine acetylation / cellular response to L-leucine / histone H3 acetyltransferase activity / NFE2L2 regulating ER-stress associated genes / peptide N-acetyltransferase activity / acetylation-dependent protein binding / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / NGF-stimulated transcription / STAT3 nuclear events downstream of ALK signaling / histone H3K18 acetyltransferase activity / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / NFE2L2 regulates pentose phosphate pathway genes / TGFBR3 expression / Polo-like kinase mediated events / NFE2L2 regulating MDR associated enzymes / regulation of androgen receptor signaling pathway / regulation of mitochondrion organization / positive regulation by host of viral transcription / face morphogenesis / Regulation of FOXO transcriptional activity by acetylation / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / regulation of glycolytic process / RUNX3 regulates NOTCH signaling / Regulation of gene expression by Hypoxia-inducible Factor / Nuclear events mediated by NFE2L2 / NOTCH4 Intracellular Domain Regulates Transcription / FOXO-mediated transcription of cell death genes / Regulation of NFE2L2 gene expression / NOTCH3 Intracellular Domain Regulates Transcription / platelet formation / TRAF6 mediated IRF7 activation / peptide-lysine-N-acetyltransferase activity / megakaryocyte development / NFE2L2 regulating tumorigenic genes / NFE2L2 regulating anti-oxidant/detoxification enzymes / macrophage derived foam cell differentiation / regulation of tubulin deacetylation / nuclear androgen receptor binding / STAT family protein binding / protein acetylation / acyltransferase activity / internal protein amino acid acetylation / fat cell differentiation / positive regulation of transforming growth factor beta receptor signaling pathway / Formation of paraxial mesoderm / stimulatory C-type lectin receptor signaling pathway / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / PI5P Regulates TP53 Acetylation / acetyltransferase activity / Zygotic genome activation (ZGA) / RUNX3 regulates p14-ARF / NF-kappaB binding / histone acetyltransferase complex / negative regulation of tumor necrosis factor-mediated signaling pathway / Attenuation phase / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / somitogenesis / negative regulation of protein-containing complex assembly / negative regulation of gluconeogenesis / cellular response to nutrient levels / protein localization to CENP-A containing chromatin / canonical NF-kappaB signal transduction / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / positive regulation of T-helper 17 cell lineage commitment / pre-mRNA intronic binding / histone acetyltransferase activity / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Packaging Of Telomere Ends / regulation of cellular response to heat / histone acetyltransferase / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / skeletal muscle tissue development / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / Deposition of new CENPA-containing nucleosomes at the centromere / Regulation of TP53 Activity through Acetylation / nucleosomal DNA binding
Similarity search - Function
Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding / Zinc finger, TAZ-type / TAZ domain superfamily / TAZ zinc finger / Zinc finger TAZ-type profile. / TAZ zinc finger, present in p300 and CBP / Coactivator CBP, KIX domain / CREB-binding protein/p300, atypical RING domain ...Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding / Zinc finger, TAZ-type / TAZ domain superfamily / TAZ zinc finger / Zinc finger TAZ-type profile. / TAZ zinc finger, present in p300 and CBP / Coactivator CBP, KIX domain / CREB-binding protein/p300, atypical RING domain / CBP/p300-type histone acetyltransferase domain / CBP/p300, atypical RING domain superfamily / KIX domain / CREB-binding protein/p300, atypical RING domain / KIX domain profile. / CBP/p300-type histone acetyltransferase (HAT) domain profile. / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / Histone acetylation protein / Coactivator CBP, KIX domain superfamily / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Nuclear receptor coactivator, interlocking / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Histone H2A type 1-B/E / Histone H2B type 1-J / Histone H3.1 / Histone acetyltransferase p300
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsKikuchi M / Morita S / Wakamori M / Shin S / Uchikubo-Kamo T / Shirouzu M / Umehara T
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: 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
DepositionOct 26, 2022-
Header (metadata) releaseMay 17, 2023-
Map releaseMay 17, 2023-
UpdateJul 26, 2023-
Current statusJul 26, 2023Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_34594.png

Downloads & links

-
Map

FileDownload / File: emd_34594.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.47 Å/pix.
x 250 pix.
= 367.5 Å		1.47 Å/pix.
x 250 pix.
= 367.5 Å		1.47 Å/pix.
x 250 pix.
= 367.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.47 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.023940945 - 0.075058535
Average (Standard dev.)0.000054901502 (±0.0026756027)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 367.5 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_34594_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_34594_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_34594_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : the p300 catalytic core bound to the H4K12acK16ac nucleosome

EntireName: the p300 catalytic core bound to the H4K12acK16ac nucleosome
Components
  • Complex: the p300 catalytic core bound to the H4K12acK16ac nucleosome
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-B/E
    • Protein or peptide: Histone H2B type 1-J
    • DNA: DNA (180-mer)
    • Protein or peptide: Histone acetyltransferase p300

-
Supramolecule #1: the p300 catalytic core bound to the H4K12acK16ac nucleosome

SupramoleculeName: 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.
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Histone H3.1

MacromoleculeName: Histone H3.1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.305969 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEACEAY LVGLFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3.1

-
Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.345289 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKGGKGL G(ALY)GGA(ALY)RHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TY TEHAKRK TVTAMDVVYA LKRQGRTLYG FGG

-
Macromolecule #3: Histone H2A type 1-B/E

MacromoleculeName: Histone H2A type 1-B/E / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.034355 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
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

MacromoleculeName: Histone H2B type 1-J / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.804045 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PEPAKSAPAP KKGSKKAVTK AQKKDGKKRK RSRKESYSIY VYKVLKQVHP DTGISSKAMG IMNSFVNDIF ERIAGEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSAK

UniProtKB: Histone H2B type 1-J

-
Macromolecule #6: Histone acetyltransferase p300

MacromoleculeName: Histone acetyltransferase p300 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: histone acetyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 92.314391 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: 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)

MacromoleculeName: DNA (180-mer) / type: dna / ID: 5 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.560527 KDa
SequenceString: (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

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1kx3

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 89085
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more