+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31907 | |||||||||
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Title | Telomeric Dinucleosome at 4.6 angstroms | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.6 Å | |||||||||
Authors | Soman A | |||||||||
Funding support | Singapore, 1 items
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Citation | Journal: Nature / Year: 2022 Title: Columnar structure of human telomeric chromatin. Authors: Aghil Soman / Sook Yi Wong / Nikolay Korolev / Wahyu Surya / Simon Lattmann / Vinod K Vogirala / Qinming Chen / Nikolay V Berezhnoy / John van Noort / Daniela Rhodes / Lars Nordenskiöld / Abstract: Telomeres, the ends of eukaryotic chromosomes, play pivotal parts in ageing and cancer and are targets of DNA damage and the DNA damage response. Little is known about the structure of telomeric ...Telomeres, the ends of eukaryotic chromosomes, play pivotal parts in ageing and cancer and are targets of DNA damage and the DNA damage response. Little is known about the structure of telomeric chromatin at the molecular level. Here we used negative stain electron microscopy and single-molecule magnetic tweezers to characterize 3-kbp-long telomeric chromatin fibres. We also obtained the cryogenic electron microscopy structure of the condensed telomeric tetranucleosome and its dinucleosome unit. The structure displayed close stacking of nucleosomes with a columnar arrangement, and an unusually short nucleosome repeat length that comprised about 132 bp DNA wound in a continuous superhelix around histone octamers. This columnar structure is primarily stabilized by the H2A carboxy-terminal and histone amino-terminal tails in a synergistic manner. The columnar conformation results in exposure of the DNA helix, which may make it susceptible to both DNA damage and the DNA damage response. The conformation also exists in an alternative open state, in which one nucleosome is unstacked and flipped out, which exposes the acidic patch of the histone surface. The structural features revealed in this work suggest mechanisms by which protein factors involved in telomere maintenance can access telomeric chromatin in its compact form. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_31907.map.gz | 14.6 MB | EMDB map data format | |
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Header (meta data) | emd-31907-v30.xml emd-31907.xml | 14.9 KB 14.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_31907_fsc.xml | 5.8 KB | Display | FSC data file |
Images | emd_31907.png | 72 KB | ||
Masks | emd_31907_msk_1.map | 15.6 MB | Mask map | |
Others | emd_31907_half_map_1.map.gz emd_31907_half_map_2.map.gz | 11.1 MB 11.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31907 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31907 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_31907.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.4 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_31907_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_31907_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_31907_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Telomeric Dinucleosome
Entire | Name: Telomeric Dinucleosome |
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Components |
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-Supramolecule #1: Telomeric Dinucleosome
Supramolecule | Name: Telomeric Dinucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: Telomeric Dinucleosome
Macromolecule | Name: Telomeric Dinucleosome / type: other / ID: 1 / Classification: other |
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Sequence | String: MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSAV MALQEACEAY LVGLFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA MSG RGKGGKGLGK GGAKRHRKVL RDNIQGITKP ...String: MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSAV MALQEACEAY LVGLFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA MSG RGKGGKGLGK GGAKRHRKVL RDNIQGITKP AIRRLARRGG VKRISGLIYE ETRGVLKVFL ENVIRDAVTY TEHAKRKTVT AMDVVYALKR QGRTLYGFGG MSGRGKQGG KARAKAKTRS SRAGLQFPVG RVHRLLRKGN YSERVGAGAP VYLAAVLEYL TAEILELAGN AARDNKKTRI IPRHLQLAIR NDEELNKLLG RVTIAQGGVL PNIQAVLLPK KTESHHKAKG K MPEPAKSA PAPKKGSKKA VTKAQKKDGK KRKRSRKESY SVYVYKVLKQ VHPDTGISSK AMGIMNSFVN DIFERIAGEA SRLAHYNKRS TITSREIQTA VRLLLPGELA KHAVSEGTKA VTKYTSAK G GGTTAGGGTT AGGGTTAGGG TTAGGGTTAG GGTTAGGGTT AGGGTTAGGG TTAGGGTTAG GGTTAGGGTT AGGGTTAGGG TTAGGGTTAG GGTTAGGGTT AGGGTTAGGG TTAGGGTTAG GGTTAGGGTT AGGGTTAGGG TTAGGGTTAG GGTTAGGGTT AGGGTTAGGG TTAGGGTTAG GGTTAGGGTT AGGGTTAGGG TTAGGGTTAG GGTTAGGGTT AGGGTTAGGG TTAGGGTTAG GGTTAGGGTT AGGGTTAGGG TTAGGGTTAG GGTT AACCC TAACCCTAAC CCTAACCCTA ACCCTAACCC TAACCCTAAC CCTAACCCTA ACCCTAACCC TAACCCTAAC CCTAACCCTA ACCCTAACCC TAACCCTAAC CCTAACCCTA ACCCTAACCC TAACCCTAAC CCTAACCCTA ACCCTAACCC TAACCCTAAC CCTAACCCTA ACCCTAACCC TAACCCTAAC CCTAACCCTA ACCCTAACCC TAACCCTAAC CCTAACCCTA ACCCTAACCC TAACCCTAAC CCTAACCCTA ACCCTAACCC |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 6 |
Grid | Model: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Initial model | PDB ID: |
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Refinement | Protocol: RIGID BODY FIT |