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Open data
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Basic information
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Title | Telomeric Dinucleosome in open state | |||||||||
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![]() | Nucleosome / Telomere / Chromatin / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | |||||||||
Function / homology | ![]() negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / 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 / nucleosomal DNA binding / Deposition of new CENPA-containing nucleosomes at the centromere ...negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / 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 / nucleosomal DNA binding / 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 / Interleukin-7 signaling / epigenetic regulation of gene expression / 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 / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / innate immune response in mucosa / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / heterochromatin formation / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / UCH proteinases / antimicrobial humoral immune response mediated by antimicrobial peptide / nucleosome / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / gene expression / HATs acetylate histones / antibacterial humoral response / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / defense response to Gram-negative bacterium / Estrogen-dependent gene expression / killing of cells of another organism / chromosome, telomeric region / Ub-specific processing proteases / defense response to Gram-positive bacterium / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / negative regulation of cell population proliferation / protein-containing complex / DNA binding / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||
![]() | Soman A | |||||||||
Funding support | ![]()
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![]() | ![]() 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. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
Map data | ![]() | 116.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20 KB 20 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.4 KB | Display | ![]() |
Images | ![]() | 54.7 KB | ||
Masks | ![]() | 125 MB | ![]() | |
Filedesc metadata | ![]() | 5.5 KB | ||
Others | ![]() ![]() | 98.5 MB 98.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7v9cMC ![]() 7v90C ![]() 7v96C ![]() 7v9jC ![]() 7v9kC ![]() 7v9sC ![]() 7va4C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.858 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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-Half map: #2
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-Half map: #1
File | emd_31815_half_map_2.map | ||||||||||||
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Sample components
-Entire : Telomeric Dinucleosome in open state
Entire | Name: Telomeric Dinucleosome in open state |
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Components |
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-Supramolecule #1: Telomeric Dinucleosome in open state
Supramolecule | Name: Telomeric Dinucleosome in open state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: DNA (275-mer)
Macromolecule | Name: DNA (275-mer) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 87.465484 KDa |
Sequence | String: (DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT) (DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG) (DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT) (DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG) (DT) (DT)(DA)(DG)(DG)(DG)(DT) ...String: (DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT) (DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG) (DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT) (DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG) (DT) (DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA) (DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT) (DT)(DA) (DG)(DG)(DG)(DT)(DT)(DA)(DG) (DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT) (DA)(DG)(DG) (DG)(DT)(DT)(DA)(DG)(DG) (DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA) (DG)(DG)(DG)(DT) (DT)(DA)(DG)(DG)(DG) (DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG) (DG)(DG)(DT)(DT)(DA) (DG)(DG)(DG)(DT) (DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG) (DG)(DT)(DT)(DA)(DG)(DG) (DG)(DT)(DT) (DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG) (DT)(DT)(DA)(DG)(DG)(DG)(DT) (DT)(DA) (DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT) (DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA) (DG) (DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT) (DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG) (DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA) (DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT) (DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG) (DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT) (DA) (DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG) (DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT)(DA) (DG)(DG) (DG)(DT)(DT)(DA)(DG)(DG)(DG) (DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT) |
-Macromolecule #2: DNA (275-mer)
Macromolecule | Name: DNA (275-mer) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 82.365664 KDa |
Sequence | String: (DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC) (DC)(DT)(DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA) (DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC)(DC) (DT)(DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA)(DC) (DC) (DC)(DT)(DA)(DA)(DC)(DC) ...String: (DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC) (DC)(DT)(DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA) (DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC)(DC) (DT)(DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA)(DC) (DC) (DC)(DT)(DA)(DA)(DC)(DC)(DC)(DT) (DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC) (DC)(DT) (DA)(DA)(DC)(DC)(DC)(DT)(DA) (DA)(DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC)(DC) (DT)(DA)(DA) (DC)(DC)(DC)(DT)(DA)(DA) (DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC)(DC)(DT) (DA)(DA)(DC)(DC) (DC)(DT)(DA)(DA)(DC) (DC)(DC)(DT)(DA)(DA)(DC)(DC)(DC)(DT)(DA) (DA)(DC)(DC)(DC)(DT) (DA)(DA)(DC)(DC) (DC)(DT)(DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA) (DC)(DC)(DC)(DT)(DA)(DA) (DC)(DC)(DC) (DT)(DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA)(DC) (DC)(DC)(DT)(DA)(DA)(DC)(DC) (DC)(DT) (DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC) (DC)(DT)(DA)(DA)(DC)(DC)(DC)(DT) (DA) (DA)(DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC)(DC) (DT)(DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA) (DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC)(DC)(DT) (DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC) (DC)(DT)(DA)(DA)(DC)(DC)(DC)(DT)(DA) (DA)(DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC)(DC) (DT) (DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA) (DC)(DC)(DC)(DT)(DA)(DA)(DC)(DC)(DC)(DT) (DA)(DA) (DC)(DC)(DC)(DT)(DA)(DA)(DC) (DC)(DC)(DT)(DA)(DA)(DC)(DC)(DC) |
-Macromolecule #3: Histone H3.1
Macromolecule | Name: Histone H3.1 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 15.437167 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEACEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA UniProtKB: Histone H3.1 |
-Macromolecule #4: Histone H4
Macromolecule | Name: Histone H4 / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 11.394426 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG UniProtKB: Histone H4 |
-Macromolecule #5: Histone H2A type 1-B/E
Macromolecule | Name: Histone H2A type 1-B/E / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 14.165551 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSGRGKQGGK ARAKAKTRSS RAGLQFPVGR VHRLLRKGNY SERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIR NDEELNKLLG RVTIAQGGVL PNIQAVLLPK KTESHHKAKG K UniProtKB: Histone H2A type 1-B/E |
-Macromolecule #6: Histone H2B type 1-K
Macromolecule | Name: Histone H2B type 1-K / type: protein_or_peptide / ID: 6 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 10.607174 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: RSRKESYSVY VYKVLKQVHP DTGISSKAMG IMNSFVNDIF ERIAGEASRL AHYNKRSTIT SREIQTAVRL LLPGELAKHA VSEGTKAVT KYTSAK UniProtKB: Histone H2B type 1-K |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 6 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |