+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4105 | |||||||||
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Title | TRF1 apo | |||||||||
Map data | Negative stain EM structure of the full length TRF1 protein | |||||||||
Sample |
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Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 23.0 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_4105.map.gz | 1.7 MB | EMDB map data format | |
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Header (meta data) | emd-4105-v30.xml emd-4105.xml | 11.9 KB 11.9 KB | Display Display | EMDB header |
Images | emd_4105.png | 145.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4105 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4105 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_4105.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Negative stain EM structure of the full length TRF1 protein | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 dimer
Entire | Name: TRF1 dimer |
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Components |
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-Supramolecule #1: TRF1 dimer
Supramolecule | Name: TRF1 dimer / type: complex / ID: 1 / Parent: 0 |
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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: Nagatively stained images were prepared using standard 1% Uranyl-acetate staining procedure | ||||||||||||
Grid | Model: Electron Microscopy SciencesCF400-CU / 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: 61320 |
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 / Average exposure time: 1.0 sec. / Average electron dose: 15.0 e/Å2 |
-Image processing
Particle selection | Number selected: 32880 Details: We have used eider semi-automatic particle selection implemented in EMAN2 or manual particle selection implemented in EMAN1 |
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CTF correction | Software - Name: CTFFIND (ver. 3) |
Startup model | Type of model: OTHER Details: We used reference free 2D averages as intup into the program e2initialmodel.py implemented in EMAN2 with C2 symmetry |
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: 23.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Xmipp (ver. 2.4) / Number images used: 10769 |
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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