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Yorodumi- EMDB-2601: Cryo-EM study of the chromatin fiber reveals a double helix twist... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2601 | |||||||||
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Title | Cryo-EM study of the chromatin fiber reveals a double helix twisted by tetra-nucleosomal units | |||||||||
Map data | Reconstruction of 12x187 bp chromatin | |||||||||
Sample |
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Keywords | In vitro reconstituted 12x187 bp chromatin | |||||||||
Biological species | Xenopus laevis (African clawed frog) / Homo sapiens (human) / unidentified (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 11.0 Å | |||||||||
Authors | Song F / Chen P / Sun D / Wang M / Dong L / Liang D / Xu RM / Zhu P / Li G | |||||||||
Citation | Journal: Science / Year: 2014 Title: Cryo-EM study of the chromatin fiber reveals a double helix twisted by tetranucleosomal units. Authors: Feng Song / Ping Chen / Dapeng Sun / Mingzhu Wang / Liping Dong / Dan Liang / Rui-Ming Xu / Ping Zhu / Guohong Li / Abstract: The hierarchical packaging of eukaryotic chromatin plays a central role in transcriptional regulation and other DNA-related biological processes. Here, we report the 11-angstrom-resolution cryogenic ...The hierarchical packaging of eukaryotic chromatin plays a central role in transcriptional regulation and other DNA-related biological processes. Here, we report the 11-angstrom-resolution cryogenic electron microscopy (cryo-EM) structures of 30-nanometer chromatin fibers reconstituted in the presence of linker histone H1 and with different nucleosome repeat lengths. The structures show a histone H1-dependent left-handed twist of the repeating tetranucleosomal structural units, within which the four nucleosomes zigzag back and forth with a straight linker DNA. The asymmetric binding and the location of histone H1 in chromatin play a role in the formation of the 30-nanometer fiber. Our results provide mechanistic insights into how nucleosomes compact into higher-order chromatin fibers. | |||||||||
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_2601.map.gz | 151.9 MB | EMDB map data format | |
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Header (meta data) | emd-2601-v30.xml emd-2601.xml | 10.5 KB 10.5 KB | Display Display | EMDB header |
Images | emd_2601.png emd_2601_1.png | 222.5 KB 236.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2601 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2601 | HTTPS FTP |
-Validation report
Summary document | emd_2601_validation.pdf.gz | 241.4 KB | Display | EMDB validaton report |
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Full document | emd_2601_full_validation.pdf.gz | 240.5 KB | Display | |
Data in XML | emd_2601_validation.xml.gz | 6.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2601 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2601 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2601.map.gz / Format: CCP4 / Size: 162.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of 12x187 bp chromatin | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.539 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 : In vitro reconstituted 12x187 bp chromatin
Entire | Name: In vitro reconstituted 12x187 bp chromatin |
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Components |
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-Supramolecule #1000: In vitro reconstituted 12x187 bp chromatin
Supramolecule | Name: In vitro reconstituted 12x187 bp chromatin / type: sample / ID: 1000 / Oligomeric state: Dodecamer / Number unique components: 3 |
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-Macromolecule #1: Core histone
Macromolecule | Name: Core histone / type: protein_or_peptide / ID: 1 Details: Octameric nucleosome core histone contains 2 copies histone H2A, H2B, H3 and H4. 12 octamer units constitutes the dodecamer. Number of copies: 2 / Oligomeric state: Octamer / Recombinant expression: Yes |
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Source (natural) | Organism: Xenopus laevis (African clawed frog) / Location in cell: Nucleus |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
-Macromolecule #2: Histone H1.4
Macromolecule | Name: Histone H1.4 / type: protein_or_peptide / ID: 2 / Name.synonym: HISTIHIE Details: Each octamer contains 1 copy linker histone, histone H1.4 Number of copies: 12 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Location in cell: Nucleus |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
-Macromolecule #3: 601 DNA
Macromolecule | Name: 601 DNA / type: dna / ID: 3 / Details: 12 tandem repeats; full length 2244 bp / Classification: DNA / Structure: DOUBLE HELIX / Synthetic?: No |
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Source (natural) | Organism: unidentified (others) |
Sequence | String: CTCGGGTGAT GCCGGATCCC CTGGAGAATC CCGGTGCCGA GGCCGCTCAA TTGGTCGTAG ACAGCTCTAG CACCGCTTAA ACGCACGTAC GCGCTGTCCC CCGCGTTTTA ACCGCCAAGG GGATTACTCC CTAGTCTCCA GGCACGTGTC ACATATATAC ATCCTGTTCC AGTGCCGGTG TCGCTTG |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 / Details: 10 mM HEPES, pH 8.0, 0.1 mM EDTA |
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Grid | Details: 300 mesh R2.1 Quantifoil holey grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV Method: Sample absorbed for 1 to 1.5 min, blotted for 4 seconds before plunging |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 155,000 times magnification |
Details | Parallel beam illumination |
Date | Apr 1, 2012 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 6100 / Average electron dose: 18 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.2 µm / Nominal defocus min: 1.45 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: CTF correction of each particle |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 11.0 Å / Resolution method: OTHER / Software - Name: EMAN2 / Number images used: 28000 |