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Yorodumi- EMDB-17253: Structure of TRF1core in complex with telomeric nucleosome (4:1 c... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17253 | ||||||||||||
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Title | Structure of TRF1core in complex with telomeric nucleosome (4:1 complex) | ||||||||||||
Map data | Postprocess map of TRF1-TeloNCP 4:1 complex | ||||||||||||
Sample |
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Keywords | Telomeric nucleosome / shelterin / telomere / DNA BINDING PROTEIN | ||||||||||||
Function / homology | Function and homology information 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 / Deposition of new CENPA-containing nucleosomes at the centromere / nucleosomal DNA binding ...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 / Deposition of new CENPA-containing nucleosomes at the centromere / nucleosomal DNA binding / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / telomere organization / Meiotic synapsis / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / Regulation of endogenous retroelements by KRAB-ZFP proteins / 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 / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / 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 / DNA Damage/Telomere Stress Induced Senescence / heterochromatin formation / PKMTs methylate histone lysines / Metalloprotease DUBs / 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 / antibacterial humoral response / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / gene expression / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / 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 / identical protein binding / membrane / nucleus / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.67 Å | ||||||||||||
Authors | Hu H / van Roon AMM / Ghanim GE / Ahsan B / Oluwole A / Peak-Chew S / Robinson CV / Nguyen THD | ||||||||||||
Funding support | United Kingdom, European Union, United States, 3 items
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Citation | Journal: Sci Adv / Year: 2023 Title: Structural basis of telomeric nucleosome recognition by shelterin factor TRF1. Authors: Hongmiao Hu / Anne-Marie M van Roon / George E Ghanim / Bilal Ahsan / Abraham O Oluwole / Sew-Yeu Peak-Chew / Carol V Robinson / Thi Hoang Duong Nguyen / Abstract: Shelterin and nucleosomes are the key players that organize mammalian chromosome ends into the protective telomere caps. However, how they interact with each other at telomeres remains unknown. We ...Shelterin and nucleosomes are the key players that organize mammalian chromosome ends into the protective telomere caps. However, how they interact with each other at telomeres remains unknown. We report cryo-electron microscopy structures of a human telomeric nucleosome both unbound and bound to the shelterin factor TRF1. Our structures reveal that TRF1 binds unwrapped nucleosomal DNA ends by engaging both the nucleosomal DNA and the histone octamer. Unexpectedly, TRF1 binding shifts the register of the nucleosomal DNA by 1 bp. We discovered that phosphorylation of the TRF1 C terminus and a noncanomical DNA binding surface on TRF1 are critical for its association with telomeric nucleosomes. These insights into shelterin-chromatin interactions have crucial implications for understanding telomeric chromatin organization and other roles of shelterin at telomeres including replication and transcription. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17253.map.gz | 257.4 MB | EMDB map data format | |
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Header (meta data) | emd-17253-v30.xml emd-17253.xml | 29.1 KB 29.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17253_fsc.xml | 15 KB | Display | FSC data file |
Images | emd_17253.png | 85 KB | ||
Others | emd_17253_additional_1.map.gz emd_17253_half_map_1.map.gz emd_17253_half_map_2.map.gz | 225.4 MB 226.6 MB 226.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17253 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17253 | HTTPS FTP |
-Validation report
Summary document | emd_17253_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_17253_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_17253_validation.xml.gz | 22.1 KB | Display | |
Data in CIF | emd_17253_validation.cif.gz | 29.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17253 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17253 | HTTPS FTP |
-Related structure data
Related structure data | 8ox0C 8ox1C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_17253.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Postprocess map of TRF1-TeloNCP 4:1 complex | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.826 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Refine3D map of TRF1-TeloNCP 4:1 complex
File | emd_17253_additional_1.map | ||||||||||||
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Annotation | Refine3D map of TRF1-TeloNCP 4:1 complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map of TRF1-TeloNCP 4:1 complex
File | emd_17253_half_map_1.map | ||||||||||||
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Annotation | half map of TRF1-TeloNCP 4:1 complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map of TRF1-TeloNCP 4:1 complex
File | emd_17253_half_map_2.map | ||||||||||||
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Annotation | half map of TRF1-TeloNCP 4:1 complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : TRF1core in complex with telomeric nucleosome
+Supramolecule #1: TRF1core in complex with telomeric nucleosome
+Supramolecule #2: Human telomeric nucleosome
+Supramolecule #3: Human TRF1core complex
+Macromolecule #1: Human Histone H3
+Macromolecule #2: Human histone H4
+Macromolecule #3: Human Histone H2A
+Macromolecule #4: Human histone H2B
+Macromolecule #7: Human TRF1 protein
+Macromolecule #5: Telomeric DNA G strand
+Macromolecule #6: Telomeric DNA C strand
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 Component:
Details: 25 mM HEPES-KOH pH 8.0, 150 mM KCl, 1 mM MgCl2, 1% glycerol, 0.01% Igepal CA-630, 1 mM DTT | |||||||||||||||||||||
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Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY | |||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: Blot Force: -15 Blot Time: 2.5 s. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 78.0 K |
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Software | Name: EPU (ver. 2.13.0.3175REL) |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 24566 / Average exposure time: 2.25 sec. / Average electron dose: 56.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |