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- EMDB-36390: Cryo-EM structure of the human nucleosome lacking N-terminal regi... -
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Open data
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Basic information
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Title | Cryo-EM structure of the human nucleosome lacking N-terminal region of H2A, H2B, H3, and H4 | |||||||||||||||||||||
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![]() | nuclear protein / chromatin / GENE REGULATION-DNA COMPLEX | |||||||||||||||||||||
Function / homology | ![]() 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 / nucleosomal DNA binding ...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 / nucleosomal DNA binding / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / innate immune response in mucosa / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / heterochromatin formation / 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 / Metalloprotease DUBs / PKMTs methylate histone lysines / 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 / 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 / gene expression / HATs acetylate histones / Processing of DNA double-strand break ends / antibacterial humoral response / 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 | |||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.44 Å | |||||||||||||||||||||
![]() | Oishi T / Hatazawa S / Kujirai T / Kato J / Kobayashi Y / Ogasawara M / Akatsu M / Takizawa Y / Kurumizaka H | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 33.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 24.3 KB 24.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.6 KB | Display | ![]() |
Images | ![]() | 70 KB | ||
Filedesc metadata | ![]() | 6.4 KB | ||
Others | ![]() ![]() ![]() | 7.4 MB 40.8 MB 40.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8jlaMC ![]() 8jl9C ![]() 8jlbC ![]() 8jldC 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: 1.06 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_36390_additional_1.map | ||||||||||||
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Density Histograms |
-Half map: #1
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Density Histograms |
-Half map: #2
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Density Histograms |
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Sample components
-Entire : The human nucleosome lacking N-terminal region of H2A, H2B, H3, a...
Entire | Name: The human nucleosome lacking N-terminal region of H2A, H2B, H3, and H4 with scFv |
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Components |
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-Supramolecule #1: The human nucleosome lacking N-terminal region of H2A, H2B, H3, a...
Supramolecule | Name: 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 |
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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: 12.816991 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GSHMSAPATG GVKKPHRYRP GTVALREIRR YQKSTELLIR KLPFQRLVRE IAQDFKTDLR FQSSAVMALQ EACEAYLVGL FEDTNLCAI HAKRVTIMPK DIQLARRIRG ERA 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: ![]() |
Molecular weight | Theoretical: 10.404241 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GSHMKRHRKV LRDNIQGITK PAIRRLARRG GVKRISGLIY EETRGVLKVF LENVIRDAVT YTEHAKRKTV TAMDVVYALK RQGRTLYGF GG UniProtKB: Histone H4 |
-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: 13.58886 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GSHMARAKAK TRSSRAGLQF PVGRVHRLLR KGNYSERVGA GAPVYLAAVL EYLTAEILEL AGNAARDNKK TRIIPRHLQL AIRNDEELN KLLGRVTIAQ GGVLPNIQAV LLPKKTESHH KAKGK 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: 11.751545 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GSHMDGKKRK RSRKESYSIY VYKVLKQVHP DTGISSKAMG IMNSFVNDIF ERIAGEASRL AHYNKRSTIT SREIQTAVRL LLPGELAKH AVSEGTKAVT KYTSAK UniProtKB: Histone H2B type 1-J |
-Macromolecule #5: DNA (193-MER)
Macromolecule | Name: DNA (193-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 59.589984 KDa |
Sequence | 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) ...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) |
-Macromolecule #6: DNA (193-MER)
Macromolecule | Name: DNA (193-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 59.580969 KDa |
Sequence | 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) ...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) |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
Details | Human nucleosome lacking N-terminal region of H2A, H2B, H3, and H4 aided by scFv |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 59.3 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination 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 |