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- EMDB-36390: Cryo-EM structure of the human nucleosome lacking N-terminal regi... -

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Entry
Database: EMDB / ID: EMD-36390
TitleCryo-EM structure of the human nucleosome lacking N-terminal region of H2A, H2B, H3, and H4
Map data
Sample
  • Complex: The human nucleosome lacking N-terminal region of H2A, H2B, H3, and H4 with scFv
    • 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 (193-MER)
    • DNA: DNA (193-MER)
Keywordsnuclear protein / chromatin / GENE REGULATION-DNA COMPLEX
Function / homology
Function and homology information


negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / 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 ...negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / 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 / nucleosomal DNA binding / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / telomere organization / Meiotic synapsis / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / HCMV Late Events / innate immune response in mucosa / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / heterochromatin formation / PKMTs methylate histone lysines / Metalloprotease DUBs / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / UCH proteinases / antimicrobial humoral immune response mediated by antimicrobial peptide / nucleosome / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / antibacterial humoral response / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Processing of DNA double-strand break ends / gene expression / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / defense response to Gram-negative bacterium / Estrogen-dependent gene expression / killing of cells of another organism / chromosome, telomeric region / Ub-specific processing proteases / defense response to Gram-positive bacterium / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / negative regulation of cell population proliferation / protein-containing complex / DNA binding / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol
Similarity search - Function
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 H4, conserved site / Histone H4 signature. / Histone H4 ...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 H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / Histone H2A / Histone 2A / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / 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
Similarity search - Domain/homology
Histone H2A type 1-B/E / Histone H2B type 1-J / Histone H4 / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsOishi T / Hatazawa S / Kujirai T / Kato J / Kobayashi Y / Ogasawara M / Akatsu M / Takizawa Y / Kurumizaka H
Funding support Japan, 6 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP18H05534 Japan
Japan Society for the Promotion of Science (JSPS)JP19K06522 Japan
Japan Society for the Promotion of Science (JSPS)JP20K15711 Japan
Japan Society for the Promotion of Science (JSPS)JP23H05475 Japan
Japan Science and TechnologyJPMJER1901 Japan
Japan Agency for Medical Research and Development (AMED)JP23ama121009 Japan
CitationJournal: Nucleic Acids Res / Year: 2023
Title: Contributions of histone tail clipping and acetylation in nucleosome transcription by RNA polymerase II.
Authors: Takumi Oishi / Suguru Hatazawa / Tomoya Kujirai / Junko Kato / Yuki Kobayashi / Mitsuo Ogasawara / Munetaka Akatsu / Haruhiko Ehara / Shun-Ichi Sekine / Gosuke Hayashi / Yoshimasa Takizawa / ...Authors: Takumi Oishi / Suguru Hatazawa / Tomoya Kujirai / Junko Kato / Yuki Kobayashi / Mitsuo Ogasawara / Munetaka Akatsu / Haruhiko Ehara / Shun-Ichi Sekine / Gosuke Hayashi / Yoshimasa Takizawa / Hitoshi Kurumizaka /
Abstract: The N-terminal tails of histones protrude from the nucleosome core and are target sites for histone modifications, such as acetylation and methylation. Histone acetylation is considered to enhance ...The N-terminal tails of histones protrude from the nucleosome core and are target sites for histone modifications, such as acetylation and methylation. Histone acetylation is considered to enhance transcription in chromatin. However, the contribution of the histone N-terminal tail to the nucleosome transcription by RNA polymerase II (RNAPII) has not been clarified. In the present study, we reconstituted nucleosomes lacking the N-terminal tail of each histone, H2A, H2B, H3 or H4, and performed RNAPII transcription assays. We found that the N-terminal tail of H3, but not H2A, H2B and H4, functions in RNAPII pausing at the SHL(-5) position of the nucleosome. Consistently, the RNAPII transcription assay also revealed that the nucleosome containing N-terminally acetylated H3 drastically alleviates RNAPII pausing at the SHL(-5) position. In addition, the H3 acetylated nucleosome produced increased amounts of the run-off transcript. These results provide important evidence that the H3 N-terminal tail plays a role in RNAPII pausing at the SHL(-5) position of the nucleosome, and its acetylation directly alleviates this nucleosome barrier.
History
DepositionJun 2, 2023-
Header (metadata) releaseOct 4, 2023-
Map releaseOct 4, 2023-
UpdateNov 8, 2023-
Current statusNov 8, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36390.png

Downloads & links

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Map

FileDownload / File: emd_36390.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 240 pix.
= 254.4 Å		1.06 Å/pix.
x 240 pix.
= 254.4 Å		1.06 Å/pix.
x 240 pix.
= 254.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.01706908 - 1.6548127
Average (Standard dev.)0.002632342 (±0.032579634)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 254.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_36390_additional_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_36390_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_36390_half_map_2.map
Projections & Slices
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Slices (1/2)
Density Histograms

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Histogram (log scale)

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Sample components

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Entire : The human nucleosome lacking N-terminal region of H2A, H2B, H3, a...

EntireName: The human nucleosome lacking N-terminal region of H2A, H2B, H3, and H4 with scFv
Components
  • Complex: The human nucleosome lacking N-terminal region of H2A, H2B, H3, and H4 with scFv
    • 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 (193-MER)
    • DNA: DNA (193-MER)

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Supramolecule #1: The human nucleosome lacking N-terminal region of H2A, H2B, H3, a...

SupramoleculeName: The human nucleosome lacking N-terminal region of H2A, H2B, H3, and H4 with scFv
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Human nucleosome lacking N-terminal region of H2A, H2B, H3, and H4 with scFv
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: 12.816991 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMSAPATG GVKKPHRYRP GTVALREIRR YQKSTELLIR KLPFQRLVRE IAQDFKTDLR FQSSAVMALQ EACEAYLVGL FEDTNLCAI HAKRVTIMPK DIQLARRIRG ERA

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: 10.404241 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMKRHRKV LRDNIQGITK PAIRRLARRG GVKRISGLIY EETRGVLKVF LENVIRDAVT YTEHAKRKTV TAMDVVYALK RQGRTLYGF GG

UniProtKB: Histone H4

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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: 13.58886 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMARAKAK TRSSRAGLQF PVGRVHRLLR KGNYSERVGA GAPVYLAAVL EYLTAEILEL AGNAARDNKK TRIIPRHLQL AIRNDEELN KLLGRVTIAQ GGVLPNIQAV LLPKKTESHH KAKGK

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: 11.751545 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMDGKKRK RSRKESYSIY VYKVLKQVHP DTGISSKAMG IMNSFVNDIF ERIAGEASRL AHYNKRSTIT SREIQTAVRL LLPGELAKH AVSEGTKAVT KYTSAK

UniProtKB: Histone H2B type 1-J

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Macromolecule #5: DNA (193-MER)

MacromoleculeName: DNA (193-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 59.589984 KDa
SequenceString: (DA)(DT)(DC)(DA)(DC)(DG)(DT)(DA)(DA)(DT) (DA)(DT)(DT)(DG)(DG)(DC)(DC)(DA)(DG)(DC) (DT)(DA)(DG)(DG)(DA)(DT)(DC)(DA)(DC) (DA)(DA)(DT)(DC)(DC)(DC)(DG)(DG)(DT)(DG) (DC) (DC)(DG)(DA)(DG)(DG)(DC) ...String:
(DA)(DT)(DC)(DA)(DC)(DG)(DT)(DA)(DA)(DT) (DA)(DT)(DT)(DG)(DG)(DC)(DC)(DA)(DG)(DC) (DT)(DA)(DG)(DG)(DA)(DT)(DC)(DA)(DC) (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)(DG)(DA) (DA)(DT)(DC)(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)(DG)(DT)(DG)(DA)(DT)(DC)(DC)(DT) (DA)(DG)(DC)(DT)(DG)(DG)(DC)(DC) (DA) (DA)(DT)(DA)(DT)(DT)(DA)(DC)(DG)(DT)(DG) (DA)(DT)

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Macromolecule #6: DNA (193-MER)

MacromoleculeName: DNA (193-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 59.580969 KDa
SequenceString: (DA)(DT)(DC)(DA)(DC)(DG)(DT)(DA)(DA)(DT) (DA)(DT)(DT)(DG)(DG)(DC)(DC)(DA)(DG)(DC) (DT)(DA)(DG)(DG)(DA)(DT)(DC)(DA)(DC) (DA)(DA)(DT)(DC)(DC)(DC)(DG)(DG)(DT)(DG) (DC) (DC)(DG)(DA)(DG)(DG)(DC) ...String:
(DA)(DT)(DC)(DA)(DC)(DG)(DT)(DA)(DA)(DT) (DA)(DT)(DT)(DG)(DG)(DC)(DC)(DA)(DG)(DC) (DT)(DA)(DG)(DG)(DA)(DT)(DC)(DA)(DC) (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)(DG)(DA) (DT)(DT)(DC)(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)(DG)(DT)(DG)(DA)(DT)(DC)(DC)(DT) (DA)(DG)(DC)(DT)(DG)(DG)(DC)(DC) (DA) (DA)(DT)(DA)(DT)(DT)(DA)(DC)(DG)(DT)(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

Concentration0.2 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsHuman nucleosome lacking N-terminal region of H2A, H2B, H3, and H4 aided by scFv

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 59.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

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

7vz4


Details: 197 bp nucleosome (PDB ID: 7K61) was also used as a startup model.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 113058
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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