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- EMDB-34597: Cryo-EM structure of the CBP catalytic core bound to the H4K12acK... -

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Basic information

Entry
Database: EMDB / ID: EMD-34597
TitleCryo-EM structure of the CBP catalytic core bound to the H4K12acK16ac nucleosome, class 3
Map data
Sample
  • Complex: the CBP 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
    • Protein or peptide: CREB-binding protein
    • DNA: DNA (180-mer)
KeywordsAcetyl taransferase / Complex / Nucleosome / TRANSFERASE / TRANSFERASE-DNA complex
Function / homology
Function and homology information


peptide lactyltransferase (CoA-dependent) activity / NFE2L2 regulating ER-stress associated genes / protein N-acetyltransferase activity / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / N-terminal peptidyl-lysine acetylation / regulation of smoothened signaling pathway / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / NFE2L2 regulates pentose phosphate pathway genes / NFE2L2 regulating MDR associated enzymes ...peptide lactyltransferase (CoA-dependent) activity / NFE2L2 regulating ER-stress associated genes / protein N-acetyltransferase activity / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / N-terminal peptidyl-lysine acetylation / regulation of smoothened signaling pathway / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / NFE2L2 regulates pentose phosphate pathway genes / NFE2L2 regulating MDR associated enzymes / MRF binding / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Regulation of FOXO transcriptional activity by acetylation / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / Nuclear events mediated by NFE2L2 / NOTCH4 Intracellular Domain Regulates Transcription / Regulation of NFE2L2 gene expression / Regulation of gene expression by Hypoxia-inducible Factor / NOTCH3 Intracellular Domain Regulates Transcription / negative regulation of transcription by RNA polymerase I / TRAF6 mediated IRF7 activation / NFE2L2 regulating tumorigenic genes / NFE2L2 regulating anti-oxidant/detoxification enzymes / protein-lysine-acetyltransferase activity / embryonic digit morphogenesis / protein acetylation / homeostatic process / Notch-HLH transcription pathway / Formation of paraxial mesoderm / positive regulation of transforming growth factor beta receptor signaling pathway / histone acetyltransferase activity / acetyltransferase activity / FOXO-mediated transcription of cell death genes / stimulatory C-type lectin receptor signaling pathway / Zygotic genome activation (ZGA) / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / histone acetyltransferase complex / canonical NF-kappaB signal transduction / negative regulation of tumor necrosis factor-mediated signaling pathway / cellular response to nutrient levels / Attenuation phase / positive regulation of double-strand break repair via homologous recombination / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / CENP-A containing nucleosome / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / regulation of cellular response to heat / histone acetyltransferase / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / : / Regulation of lipid metabolism by PPARalpha / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / NPAS4 regulates expression of target genes / Deposition of new CENPA-containing nucleosomes at the centromere / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / telomere organization / Transcriptional and post-translational regulation of MITF-M expression and activity / Inhibition of DNA recombination at telomere / CD209 (DC-SIGN) signaling / Meiotic synapsis / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / BMAL1:CLOCK,NPAS2 activates circadian expression / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / innate immune response in mucosa / SUMOylation of transcription cofactors / DNA methylation / Activation of gene expression by SREBF (SREBP) / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / epigenetic regulation of gene expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs)
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 / : / Histone acetyltransferase p300-like, PHD 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 / : / Histone acetyltransferase p300-like, PHD domain / 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 / Bromodomain, conserved site / Bromodomain signature. / Histone-fold / 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 / CREB-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 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-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34597.png

Downloads & links

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Map

FileDownload / File: emd_34597.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: 0.015
Minimum - Maximum-0.016526744 - 0.08777642
Average (Standard dev.)0.000011546847 (±0.0032580995)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Mask #1

Fileemd_34597_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_34597_half_map_1.map
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Half map: #2

Fileemd_34597_half_map_2.map
Projections & Slices
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Sample components

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Entire : the CBP catalytic core bound to the H4K12acK16ac nucleosome

EntireName: the CBP catalytic core bound to the H4K12acK16ac nucleosome
Components
  • Complex: the CBP 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
    • Protein or peptide: CREB-binding protein
    • DNA: DNA (180-mer)

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Supramolecule #1: the CBP catalytic core bound to the H4K12acK16ac nucleosome

SupramoleculeName: the CBP catalytic core bound to the H4K12acK16ac nucleosome
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: CBP was expressed in insect cells.
Source (natural)Organism: Homo sapiens (human)

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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

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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

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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

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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

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Macromolecule #5: CREB-binding protein

MacromoleculeName: CREB-binding protein / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: histone acetyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 92.690906 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GSSGSSGIFK PEELRQALMP TLEALYRQDP ESLPFRQPVD PQLLGIPDYF DIVKNPMDLS TIKRKLDTGQ YQEPWQYVDD VWLMFNNAW LYNRKTSRVY KFCSKLAEVF EQEIDPVMQS LGYCCGRKYE FSPQTLCCYG KQLCTIPRDA AYYSYQNRYH F CEKCFTEI ...String:
GSSGSSGIFK PEELRQALMP TLEALYRQDP ESLPFRQPVD PQLLGIPDYF DIVKNPMDLS TIKRKLDTGQ YQEPWQYVDD VWLMFNNAW LYNRKTSRVY KFCSKLAEVF EQEIDPVMQS LGYCCGRKYE FSPQTLCCYG KQLCTIPRDA AYYSYQNRYH F CEKCFTEI QGENVTLGDD PSQPQTTISK DQFEKKKNDT LDPEPFVDCK ECGRKMHQIC VLHYDIIWPS GFVCDNCLKK TG RPRKENK FSAKRLQTTR LGNHLEDRVN KFLRRQNHPE AGEVFVRVVA SSDKTVEVKP GMKSRFVDSG EMSESFPYRT KAL FAFEEI DGVDVCFFGM HVQEYGSDCP PPNTRRVYIS YLDSIHFFRP RCLRTAVYHE ILIGYLEYVK KLGYVTGHIW ACPP SEGDD YIFHCHPPDQ KIPKPKRLQE WYKKMLDKAF AERIIHDYKD IFKQATEDRL TSAKELPYFE GDFWPNVLEE SIKEL EQEE EERKKEESTA ASETTEGSQG DSKNAKKKNN KKTNKNKSSI SRANKKKPSM PNVSNDLSQK LYATMEKHKE VFFVIH LHA GPVINTLPPI VDPDPLLSCD LMDGRDAFLT LARDKHWEFS SLRRSKWSTL CMLVELHTQG QDRFVYTCNE CKHHVET RW HCTVCEDYDL CINCYNTKSH AHKMVKWGLG LDDEGSSQGE PQSKSPQESR RLSIQRCIQS LVHACQCRNA NCSLPSCQ K MKRVVQHTKG CKRKTNGGCP VCKQLIALCC YHAKHCQENK CPVPFCLNIK HKLRQQQIQH RLQQAQLMRR RMATMN

UniProtKB: CREB-binding protein

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Macromolecule #6: DNA (180-mer)

MacromoleculeName: DNA (180-mer) / type: dna / ID: 6 / 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)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE

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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

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Image processing

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

1kx3

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 207123
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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