+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17252 | ||||||||||||
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Title | Structure of TRF1core in complex with telomeric nucleosome | ||||||||||||
Map data | Postprocess map of TRF1core-TeloNCP 2:1 complex | ||||||||||||
Sample |
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Keywords | Telomeric nucleosome / shelterin / telomere / DNA BINDING PROTEIN | ||||||||||||
Function / homology | Function and homology information positive regulation of shelterin complex assembly / negative regulation of establishment of protein localization to telomere / negative regulation of establishment of RNA localization to telomere / negative regulation of establishment of protein-containing complex localization to telomere / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of exonuclease activity / negative regulation of telomeric D-loop disassembly / meiotic telomere clustering / telomerase activity / t-circle formation ...positive regulation of shelterin complex assembly / negative regulation of establishment of protein localization to telomere / negative regulation of establishment of RNA localization to telomere / negative regulation of establishment of protein-containing complex localization to telomere / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of exonuclease activity / negative regulation of telomeric D-loop disassembly / meiotic telomere clustering / telomerase activity / t-circle formation / telomeric D-loop disassembly / shelterin complex / Telomere C-strand synthesis initiation / double-stranded telomeric DNA binding / Telomere C-strand (Lagging Strand) Synthesis / negative regulation of telomerase activity / positive regulation of telomere maintenance / nuclear telomere cap complex / ankyrin repeat binding / Processive synthesis on the C-strand of the telomere / Polymerase switching on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / G-rich strand telomeric DNA binding / telomere capping / DNA binding, bending / negative regulation of telomere maintenance via telomere lengthening / telomeric DNA binding / negative regulation of DNA replication / negative regulation of telomere maintenance via telomerase / Telomere Extension By Telomerase / telomere maintenance via telomerase / 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 / heterochromatin organization / epigenetic regulation of gene expression / 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 / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / telomere maintenance / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates 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 / B-WICH complex positively regulates rRNA expression / G2/M DNA damage checkpoint / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / PKMTs methylate histone lysines / fibrillar center / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / spindle / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / antimicrobial humoral immune response mediated by antimicrobial peptide / UCH proteinases / 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 / Processing of DNA double-strand break ends / antibacterial humoral response / Senescence-Associated Secretory Phenotype (SASP) / microtubule binding Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 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_17252.map.gz | 259.1 MB | EMDB map data format | |
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Header (meta data) | emd-17252-v30.xml emd-17252.xml | 33 KB 33 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17252_fsc.xml | 14.8 KB | Display | FSC data file |
Images | emd_17252.png | 569 KB | ||
Others | emd_17252_additional_1.map.gz emd_17252_half_map_1.map.gz emd_17252_half_map_2.map.gz | 226.3 MB 227 MB 227 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17252 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17252 | HTTPS FTP |
-Validation report
Summary document | emd_17252_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_17252_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_17252_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | emd_17252_validation.cif.gz | 29.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17252 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17252 | HTTPS FTP |
-Related structure data
Related structure data | 8ox1MC 8ox0C M: atomic model generated by this map 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_17252.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 TRF1core-TeloNCP 2:1 complex | ||||||||||||||||||||
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 TRF1core-TeloNCP 2:1 complex
File | emd_17252_additional_1.map | ||||||||||||
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Annotation | Refine3D map of TRF1core-TeloNCP 2:1 complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map of TRF1core-TeloNCP 2:1 complex
File | emd_17252_half_map_1.map | ||||||||||||
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Annotation | half map of TRF1core-TeloNCP 2:1 complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map of TRF1core-TeloNCP 2:1 complex
File | emd_17252_half_map_2.map | ||||||||||||
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Annotation | half map of TRF1core-TeloNCP 2:1 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: Histone H3.1
+Macromolecule #2: Histone H4
+Macromolecule #3: Histone H2A type 1-C
+Macromolecule #4: Histone H2B type 1-C/E/F/G/I
+Macromolecule #7: Telomeric repeat-binding factor 1
+Macromolecule #8: Telomeric repeat-binding factor 1
+Macromolecule #5: Telomeric DNA C strand
+Macromolecule #6: Telomeric DNA G strand
+Macromolecule #9: water
-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 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 70 sec. | |||||||||||||||||||||
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 |
+Image processing
-Atomic model buiding 1
Software | Name: UCSF ChimeraX (ver. 1.5) |
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Output model | PDB-8ox1: |