+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4106 | |||||||||
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Title | TRF1-DNA | |||||||||
Map data | TRF1 bound to seven repeats of telomeric dsDNA | |||||||||
Sample |
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Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 25.0 Å | |||||||||
Authors | Boskovic J / Martinez-Gago J / Mendez-Pertuz M / Buscato A / Martinez-Torrecuadrada JL / Blasco MA | |||||||||
Citation | Journal: J Biol Chem / Year: 2016 Title: Molecular Architecture of Full-length TRF1 Favors Its Interaction with DNA. Authors: Jasminka Boskovic / Jaime Martinez-Gago / Marinela Mendez-Pertuz / Alberto Buscato / Jorge Luis Martinez-Torrecuadrada / Maria A Blasco / Abstract: Telomeres are specific DNA-protein structures found at both ends of eukaryotic chromosomes that protect the genome from degradation and from being recognized as double-stranded breaks. In ...Telomeres are specific DNA-protein structures found at both ends of eukaryotic chromosomes that protect the genome from degradation and from being recognized as double-stranded breaks. In vertebrates, telomeres are composed of tandem repeats of the TTAGGG sequence that are bound by a six-subunit complex called shelterin. Molecular mechanisms of telomere functions remain unknown in large part due to lack of structural data on shelterins, shelterin complex, and its interaction with the telomeric DNA repeats. TRF1 is one of the best studied shelterin components; however, the molecular architecture of the full-length protein remains unknown. We have used single-particle electron microscopy to elucidate the structure of TRF1 and its interaction with telomeric DNA sequence. Our results demonstrate that full-length TRF1 presents a molecular architecture that assists its interaction with telometic DNA and at the same time makes TRFH domains accessible to other TRF1 binding partners. Furthermore, our studies suggest hypothetical models on how other proteins as TIN2 and tankyrase contribute to regulate TRF1 function. | |||||||||
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_4106.map.gz | 1.7 MB | EMDB map data format | |
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Header (meta data) | emd-4106-v30.xml emd-4106.xml | 12.1 KB 12.1 KB | Display Display | EMDB header |
Images | emd_4106.png | 30 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4106 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4106 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_4106.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | TRF1 bound to seven repeats of telomeric dsDNA | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.5 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 : TRF1-DNA complex
Entire | Name: TRF1-DNA complex |
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Components |
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-Supramolecule #1: TRF1-DNA complex
Supramolecule | Name: TRF1-DNA complex / type: complex / ID: 1 / Parent: 0 Details: TRF1 protein bound to seven repeats (TTAGGG) of telomeric dsDNA |
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Source (natural) | Organism: Mus musculus (house mouse) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) / Recombinant strain: Sf9 / Recombinant plasmid: pBacPak8 |
Molecular weight | Experimental: 100 KDa |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.08 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Staining | Type: NEGATIVE / Material: Uranyl Acetate Details: Negatively stained EM specimens were prepared using standar negative staining technique with 1% UrAc | ||||||||||||
Grid | Model: Electron Microscopy Science / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
-Electron microscopy
Microscope | FEI TECNAI 12 |
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Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.2 mm / Nominal defocus max: 3.5 µm / Nominal magnification: 61350 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
Image recording | Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Sampling interval: 15.6 µm / Number grids imaged: 1 / Number real images: 397 / Average exposure time: 1.0 sec. / Average electron dose: 15.0 e/Å2 |
-Image processing
Particle selection | Number selected: 33106 |
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CTF correction | Software - Name: CTFFIND (ver. 3) |
Startup model | Type of model: OTHER Details: The same initial model as for TRF1 apo structure and band passed TRF1 apo final volume were used as an initial model for TRF1-DNA reconstructruction |
Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: EMAN (ver. 1.9) |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: Xmipp (ver. 2.4) |
Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Xmipp (ver. 2.4) / Number images used: 9918 |
Details | The selected images were normalized |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: visual inspection |
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