+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1782 | |||||||||
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Title | The nucleosome organization in native chromatin | |||||||||
Map data | helically symmetrized average | |||||||||
Sample |
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Keywords | 30-nm fibre | |||||||||
Biological species | Gallus gallus (chicken) | |||||||||
Method | subtomogram averaging / cryo EM | |||||||||
Authors | Scheffer M / Eltsov M / Frangakis A | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2011 Title: Evidence for short-range helical order in the 30-nm chromatin fibers of erythrocyte nuclei. Authors: Margot P Scheffer / Mikhail Eltsov / Achilleas S Frangakis / Abstract: Chromatin folding in eukaryotes fits the genome into the limited volume of the cell nucleus. Formation of higher-order chromatin structures attenuates DNA accessibility, thus contributing to the ...Chromatin folding in eukaryotes fits the genome into the limited volume of the cell nucleus. Formation of higher-order chromatin structures attenuates DNA accessibility, thus contributing to the control of essential genome functions such as transcription, DNA replication, and repair. The 30-nm fiber is thought to be the first hierarchical level of chromatin folding, but the nucleosome arrangement in the compact 30-nm fiber was previously unknown. We used cryoelectron tomography of vitreous sections to determine the structure of the compact, native 30-nm fiber of avian erythrocyte nuclei. The predominant geometry of the 30-nm fiber revealed by subtomogram averaging is a left-handed two-start helix with approximately 6.5 nucleosomes per 11 nm, in which the nucleosomes are juxtaposed face-to-face but are shifted off their superhelical axes with an axial translation of approximately 3.4 nm and an azimuthal rotation of approximately 54°. The nucleosomes produce a checkerboard pattern when observed in the direction perpendicular to the fiber axis but are not interdigitated. The nucleosome packing within the fibers shows larger center-to-center internucleosomal distances than previously anticipated, thus excluding the possibility of core-to-core interactions, explaining how transcription and regulation factors can access nucleosomes. | |||||||||
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_1782.map.gz | 808.3 KB | EMDB map data format | |
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Header (meta data) | emd-1782-v30.xml emd-1782.xml | 6.1 KB 6.1 KB | Display Display | EMDB header |
Images | EMD-1782.png | 87.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1782 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1782 | HTTPS FTP |
-Validation report
Summary document | emd_1782_validation.pdf.gz | 218.7 KB | Display | EMDB validaton report |
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Full document | emd_1782_full_validation.pdf.gz | 217.8 KB | Display | |
Data in XML | emd_1782_validation.xml.gz | 4.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1782 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1782 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1782.map.gz / Format: CCP4 / Size: 1001 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | helically symmetrized average | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 12 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : native chromatin fibre
Entire | Name: native chromatin fibre |
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Components |
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-Supramolecule #1000: native chromatin fibre
Supramolecule | Name: native chromatin fibre / type: sample / ID: 1000 / Number unique components: 1 |
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-Macromolecule #1: 30-nm fibre
Macromolecule | Name: 30-nm fibre / type: protein_or_peptide / ID: 1 / Name.synonym: chromatin fibre / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Gallus gallus (chicken) / synonym: Chicken |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
-Sample preparation
Vitrification | Cryogen name: NITROGEN / Instrument: OTHER |
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-Electron microscopy
Microscope | FEI POLARA 300 |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder: Eucentric / Specimen holder model: OTHER |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution method: OTHER |
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