|Entry||Database: EMDB / ID: EMD-6898|
|Title||Nucleosome with ALB1 enhancer DNA sequence, no symmetry applied|
|Map data||Nucleosome with ALB1 enhancer DNA sequence, no symmetry applied|
|Function / homology|
Function and homology information
negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / 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 / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere ...negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / 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 / 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 / telomere organization / RNA Polymerase I Promoter Opening / 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 / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / RNA Polymerase I Promoter Escape / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / NoRC negatively regulates rRNA expression / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / B-WICH complex positively regulates rRNA expression / G2/M DNA damage checkpoint / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / DNA Damage/Telomere Stress Induced Senescence / HDMs demethylate histones / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / PKMTs methylate histone lysines / HCMV Early Events / Activation of anterior HOX genes in hindbrain development during early embryogenesis / structural constituent of chromatin / Transcriptional regulation of granulopoiesis / nucleosome / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Processing of DNA double-strand break ends / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / protein heterodimerization activity / Amyloid fiber formation / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus
Similarity search - Function
Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / 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-fold
Similarity search - Domain/homology
Similarity search - Component
|Biological species||Homo sapiens (human)|
|Method||single particle reconstruction / cryo EM / Resolution: 4.5 Å|
|Authors||Takizawa Y / Tanaka H / Machida S / Koyama M / Maehara K / Ohkawa Y / Wade PA / Wolf M / Kurumizaka H|
|Citation||Journal: Open Biol / Year: 2018|
Title: Cryo-EM structure of the nucleosome containing the enhancer DNA sequence.
Authors: Yoshimasa Takizawa / Hiroki Tanaka / Shinichi Machida / Masako Koyama / Kazumitsu Maehara / Yasuyuki Ohkawa / Paul A Wade / Matthias Wolf / Hitoshi Kurumizaka /
Abstract: Pioneer transcription factors specifically target their recognition DNA sequences within nucleosomes. FoxA is the pioneer transcription factor that binds to the gene enhancer in liver precursor ...Pioneer transcription factors specifically target their recognition DNA sequences within nucleosomes. FoxA is the pioneer transcription factor that binds to the gene enhancer in liver precursor cells, and is required for liver differentiation in embryos. The enhancer DNA sequence is reportedly incorporated into nucleosomes in cells, although the nucleosome structure containing the targeting sites for FoxA has not been clarified yet. In this study, we determined the nucleosome structure containing the enhancer (N1) sequence, by cryogenic electron microscopy at 4.0 Å resolution. The nucleosome structure with the enhancer DNA is not significantly different from the previously reported nucleosome structure with the Widom 601 DNA. Interestingly, in the nucleosomes, the enhancer DNA contains local flexible regions, as compared to the Widom 601 DNA. Consistently, DNaseI treatments revealed that, in the nucleosome, the enhancer (N1) DNA is more accessible than the Widom 601 sequence. The histones also associated less strongly with the enhancer (N1) DNA than the Widom 601 DNA in the nucleosome. Therefore, the local histone-DNA contacts may be responsible for the enhanced DNA accessibility in the nucleosome with the enhancer DNA.
|Structure viewer||EM map: |
-Downloads & links
|Map data||emd_6898.map.gz||1.5 MB||EMDB map data format|
|Header (meta data)||emd-6898-v30.xml|
|FSC (resolution estimation)||emd_6898_fsc.xml||5.1 KB||Display||FSC data file|
|Summary document||emd_6898_validation.pdf.gz||78.4 KB||Display||EMDB validaton report|
|Full document||emd_6898_full_validation.pdf.gz||77.6 KB||Display|
|Data in XML||emd_6898_validation.xml.gz||493 B||Display|
-Related structure data
|Related structure data|
C: citing same article (ref.)
|Similar structure data|
|EMDB pages||EMDB (EBI/PDBe) / EMDataResource|
|Related items in Molecule of the Month|
|File||Download / File: emd_6898.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Annotation||Nucleosome with ALB1 enhancer DNA sequence, no symmetry applied|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.4 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire : Nucleosome with ALB1-DNA sequence, no symmetry applied
|Entire||Name: Nucleosome with ALB1-DNA sequence, no symmetry applied|
-Supramolecule #1: Nucleosome with ALB1-DNA sequence, no symmetry applied
|Supramolecule||Name: Nucleosome with ALB1-DNA sequence, no symmetry applied|
type: complex / ID: 1 / Parent: 0
|Source (natural)||Organism: Homo sapiens (human)|
|Recombinant expression||Organism: Escherichia coli (E. coli)|
Recombinant plasmid: pET15b-H3.1, pET15b-H4, pET15b-H2A, pET15b-H2B, pGEM-T-Easy-(186 base-pair mouse ALB1 enhancer DNA)
|Molecular weight||Theoretical: 200 KDa|
|Processing||single particle reconstruction|
|Buffer||pH: 7.5 |
|Grid||Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 100.0 nm / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 9.33 kPa / Details: Gatan Solarus|
|Vitrification||Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV / Details: 3 second blot, 2.5uL.|
|Details||sample was monodisperse|
|Microscope||FEI TALOS ARCTICA|
|Electron beam||Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN|
|Electron optics||C2 aperture diameter: 50.0 µm / Calibrated defocus max: -3.0 µm / Calibrated defocus min: -1.5 µm / Calibrated magnification: 100000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: -3.0 µm / Nominal defocus min: -1.5 µm / Nominal magnification: 73000|
|Sample stage||Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN|
|Temperature||Min: 77.0 K / Max: 100.0 K|
|Alignment procedure||Coma free - Residual tilt: 0.1 mrad|
|Details||nanoprobe, parallel beam illumination|
|Image recording||Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 2312 / Average exposure time: 2.0 sec. / Average electron dose: 80.0 e/Å2|
Model: Talos Arctica / Image courtesy: FEI Company
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