+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10390 | ||||||||||||
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Title | Structure of a human nucleosome at 3.2 A resolution | ||||||||||||
Map data | Structure of a human nucleosome at 3.2A | ||||||||||||
Sample |
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Keywords | Nucleosome / DNA / histones / NUCLEAR PROTEIN | ||||||||||||
Function / homology | Function and homology information protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / Replacement of protamines by nucleosomes in the male pronucleus / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / Packaging Of Telomere Ends / lipoxygenase pathway / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / arachidonate metabolic process ...protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / Replacement of protamines by nucleosomes in the male pronucleus / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / Packaging Of Telomere Ends / lipoxygenase pathway / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / arachidonate metabolic process / Chromatin modifying enzymes / lipid oxidation / Deposition of new CENPA-containing nucleosomes at the centromere / hepoxilin biosynthetic process / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / linoleic acid metabolic process / Meiotic synapsis / Inhibition of DNA recombination at telomere / nucleosomal DNA binding / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Interleukin-7 signaling / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / Meiotic recombination / innate immune response in mucosa / DNA Damage/Telomere Stress Induced Senescence / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Transcriptional regulation of granulopoiesis / HDMs demethylate histones / Formation of the beta-catenin:TCF transactivating complex / HCMV Early Events / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / PKMTs methylate histone lysines / B-WICH complex positively regulates rRNA expression / heterochromatin formation / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / Activation of anterior HOX genes in hindbrain development during early embryogenesis / structural constituent of chromatin / UCH proteinases / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / E3 ubiquitin ligases ubiquitinate target proteins / Senescence-Associated Secretory Phenotype (SASP) / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / antibacterial humoral response / Oxidative Stress Induced Senescence / defense response to Gram-negative bacterium / Estrogen-dependent gene expression / killing of cells of another organism / Ub-specific processing proteases / defense response to Gram-positive bacterium / protein heterodimerization activity / Amyloid fiber formation / negative regulation of cell population proliferation / DNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) / synthetic construct (others) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||
Authors | Dodonova SO / Zhu F | ||||||||||||
Funding support | Germany, 3 items
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Citation | Journal: Nature / Year: 2020 Title: Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function. Authors: Svetlana O Dodonova / Fangjie Zhu / Christian Dienemann / Jussi Taipale / Patrick Cramer / Abstract: 'Pioneer' transcription factors are required for stem-cell pluripotency, cell differentiation and cell reprogramming. Pioneer factors can bind nucleosomal DNA to enable gene expression from regions ...'Pioneer' transcription factors are required for stem-cell pluripotency, cell differentiation and cell reprogramming. Pioneer factors can bind nucleosomal DNA to enable gene expression from regions of the genome with closed chromatin. SOX2 is a prominent pioneer factor that is essential for pluripotency and self-renewal of embryonic stem cells. Here we report cryo-electron microscopy structures of the DNA-binding domains of SOX2 and its close homologue SOX11 bound to nucleosomes. The structures show that SOX factors can bind and locally distort DNA at superhelical location 2. The factors also facilitate detachment of terminal nucleosomal DNA from the histone octamer, which increases DNA accessibility. SOX-factor binding to the nucleosome can also lead to a repositioning of the N-terminal tail of histone H4 that includes residue lysine 16. We speculate that this repositioning is incompatible with higher-order nucleosome stacking, which involves contacts of the H4 tail with a neighbouring nucleosome. Our results indicate that pioneer transcription factors can use binding energy to initiate chromatin opening, and thereby facilitate nucleosome remodelling and subsequent transcription. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10390.map.gz | 9.7 MB | EMDB map data format | |
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Header (meta data) | emd-10390-v30.xml emd-10390.xml | 25.8 KB 25.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10390_fsc.xml | 6.9 KB | Display | FSC data file |
Images | emd_10390.png | 172.9 KB | ||
Filedesc metadata | emd-10390.cif.gz | 7.4 KB | ||
Others | emd_10390_half_map_1.map.gz emd_10390_half_map_2.map.gz | 9.7 MB 9.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10390 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10390 | HTTPS FTP |
-Validation report
Summary document | emd_10390_validation.pdf.gz | 962.8 KB | Display | EMDB validaton report |
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Full document | emd_10390_full_validation.pdf.gz | 962.4 KB | Display | |
Data in XML | emd_10390_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | emd_10390_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10390 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10390 | HTTPS FTP |
-Related structure data
Related structure data | 6t79MC 6t78C 6t7aC 6t7bC 6t7cC 6t7dC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10390.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Structure of a human nucleosome at 3.2A | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: half-map 2, nucleosome
File | emd_10390_half_map_1.map | ||||||||||||
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Annotation | half-map 2, nucleosome | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half-map 1, nucleosome
File | emd_10390_half_map_2.map | ||||||||||||
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Annotation | half-map 1, nucleosome | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Nucleosome
Entire | Name: Nucleosome |
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Components |
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-Supramolecule #1: Nucleosome
Supramolecule | Name: Nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Nucleosome |
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Molecular weight | Theoretical: 205 KDa |
-Supramolecule #2: Proteins
Supramolecule | Name: Proteins / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4 / Details: Proteins |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: DNA
Supramolecule | Name: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6 / Details: DNA |
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Source (natural) | Organism: synthetic construct (others) |
-Macromolecule #1: Histone H3.2
Macromolecule | Name: Histone H3.2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 15.389036 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEASEA YLVGLFEDTN LAAIHAKRVT IMPKDIQLAR RIRGERA UniProtKB: Histone H3.2 |
-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: Homo sapiens (human) |
Molecular weight | Theoretical: 11.394426 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG UniProtKB: Arachidonate 15-lipoxygenase |
-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: Homo sapiens (human) |
Molecular weight | Theoretical: 16.707277 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MGSSHHHHHH ENLYFQSNAP WMSGRGKQGG KARAKAKTRS SRAGLQFPVG RVHRLLRKGN YSERVGAGAP VYLAAVLEYL TAEILELAG NAARDNKKTR IIPRHLQLAI RNDEELNKLL GRVTIAQGGV LPNIQAVLLP KKTESHHKAK GK UniProtKB: Histone H2A type 1-B/E |
-Macromolecule #4: Histone H2B type 1-K
Macromolecule | Name: Histone H2B type 1-K / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 13.921213 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSV YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSAK UniProtKB: Histone H2B type 1-K |
-Macromolecule #5: DNA (147-MER)
Macromolecule | Name: DNA (147-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 45.240848 KDa |
Sequence | String: (DA)(DT)(DC)(DT)(DA)(DC)(DA)(DC)(DG)(DA) (DC)(DG)(DC)(DT)(DC)(DT)(DT)(DC)(DC)(DG) (DA)(DT)(DC)(DT)(DA)(DA)(DT)(DT)(DT) (DA)(DT)(DG)(DT)(DT)(DT)(DG)(DT)(DT)(DA) (DG) (DC)(DG)(DT)(DT)(DA)(DT) ...String: (DA)(DT)(DC)(DT)(DA)(DC)(DA)(DC)(DG)(DA) (DC)(DG)(DC)(DT)(DC)(DT)(DT)(DC)(DC)(DG) (DA)(DT)(DC)(DT)(DA)(DA)(DT)(DT)(DT) (DA)(DT)(DG)(DT)(DT)(DT)(DG)(DT)(DT)(DA) (DG) (DC)(DG)(DT)(DT)(DA)(DT)(DA)(DC) (DT)(DA)(DT)(DT)(DC)(DT)(DA)(DA)(DT)(DT) (DC)(DT) (DT)(DT)(DG)(DT)(DT)(DT)(DC) (DG)(DG)(DT)(DG)(DG)(DT)(DA)(DT)(DT)(DG) (DT)(DT)(DT) (DA)(DT)(DT)(DT)(DT)(DG) (DT)(DT)(DC)(DC)(DT)(DT)(DT)(DG)(DT)(DG) (DC)(DG)(DT)(DT) (DC)(DA)(DG)(DC)(DT) (DT)(DA)(DA)(DT)(DG)(DC)(DC)(DT)(DA)(DA) (DC)(DG)(DA)(DC)(DA) (DC)(DT)(DC)(DG) (DG)(DA)(DG)(DA)(DT)(DC)(DG)(DG)(DA)(DA) (DG)(DA)(DG)(DC)(DA)(DC) (DA)(DC)(DG) (DT)(DG)(DA)(DT) |
-Macromolecule #6: DNA (147-MER)
Macromolecule | Name: DNA (147-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 45.484273 KDa |
Sequence | String: (DA)(DT)(DC)(DA)(DC)(DG)(DT)(DG)(DT)(DG) (DC)(DT)(DC)(DT)(DT)(DC)(DC)(DG)(DA)(DT) (DC)(DT)(DC)(DC)(DG)(DA)(DG)(DT)(DG) (DT)(DC)(DG)(DT)(DT)(DA)(DG)(DG)(DC)(DA) (DT) (DT)(DA)(DA)(DG)(DC)(DT) ...String: (DA)(DT)(DC)(DA)(DC)(DG)(DT)(DG)(DT)(DG) (DC)(DT)(DC)(DT)(DT)(DC)(DC)(DG)(DA)(DT) (DC)(DT)(DC)(DC)(DG)(DA)(DG)(DT)(DG) (DT)(DC)(DG)(DT)(DT)(DA)(DG)(DG)(DC)(DA) (DT) (DT)(DA)(DA)(DG)(DC)(DT)(DG)(DA) (DA)(DC)(DG)(DC)(DA)(DC)(DA)(DA)(DA)(DG) (DG)(DA) (DA)(DC)(DA)(DA)(DA)(DA)(DT) (DA)(DA)(DA)(DC)(DA)(DA)(DT)(DA)(DC)(DC) (DA)(DC)(DC) (DG)(DA)(DA)(DA)(DC)(DA) (DA)(DA)(DG)(DA)(DA)(DT)(DT)(DA)(DG)(DA) (DA)(DT)(DA)(DG) (DT)(DA)(DT)(DA)(DA) (DC)(DG)(DC)(DT)(DA)(DA)(DC)(DA)(DA)(DA) (DC)(DA)(DT)(DA)(DA) (DA)(DT)(DT)(DA) (DG)(DA)(DT)(DC)(DG)(DG)(DA)(DA)(DG)(DA) (DG)(DC)(DG)(DT)(DC)(DG) (DT)(DG)(DT) (DA)(DG)(DA)(DT) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.15 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa / Details: 0.39 mB, 25 mA | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV Details: The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen ...Details: The sample was applied onto glow-discharged Quantifoil holey carbon grids. The grids were blotted from both sides for 5-10 seconds at 16*C in a chamber at 100% humidity and plunge-frozen into liquid ethane using a manual plunger.. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 30 eV |
Details | At least 50% of the data were collected at 25* stage tilt in order to partially compensate for preferred orientation of particles on the grid, and to improve angular distribution. |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average electron dose: 1.125 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |