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- EMDB-4105: TRF1 apo -

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Basic information

Entry
Database: EMDB / ID: EMD-4105
TitleTRF1 apo
Map dataNegative stain EM structure of the full length TRF1 protein
Sample
  • Complex: TRF1 dimer
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / negative staining / Resolution: 23.0 Å
AuthorsBoskovic J / Martinez-Gago J / Mendez-Pertuz M / Buscato A / Martinez-Torrecuadrada JL / Blasco MA
CitationJournal: 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
DepositionAug 23, 2016-
Header (metadata) releaseSep 7, 2016-
Map releaseSep 7, 2016-
UpdateAug 2, 2017-
Current statusAug 2, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.2
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 4.2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

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Map

FileDownload / File: emd_4105.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain EM structure of the full length TRF1 protein
Voxel sizeX=Y=Z: 2.5 Å
Density
Contour LevelBy AUTHOR: 4.2 / Movie #1: 4.2
Minimum - Maximum-4.6359134 - 10.356738
Average (Standard dev.)0.0020276885 (±0.95535845)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-40-40-40
Dimensions808080
Spacing808080
CellA=B=C: 200.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.52.52.5
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z200.000200.000200.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-40-40-40
NC/NR/NS808080
D min/max/mean-4.63610.3570.002

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Supplemental data

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Sample components

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Entire : TRF1 dimer

EntireName: TRF1 dimer
Components
  • Complex: TRF1 dimer

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Supramolecule #1: TRF1 dimer

SupramoleculeName: TRF1 dimer / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant strain: Sf9 / Recombinant plasmid: pBacPak8
Molecular weightExperimental: 100 KDa

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.08 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMTrisHCl
30.0 mMNaClSodium chloridesodium chloride
1.0 mMTCEPtris(2-carboxyethyl)phosphine
StainingType: NEGATIVE / Material: Uranyl Acetate
Details: Nagatively stained images were prepared using standard 1% Uranyl-acetate staining procedure
GridModel: Electron Microscopy SciencesCF400-CU / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR

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Electron microscopy

MicroscopeFEI TECNAI 12
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.2 mm / Nominal defocus max: 3.5 µm / Nominal magnification: 61320
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
Image recordingFilm 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

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Image processing

Particle selectionNumber selected: 32880
Details: We have used eider semi-automatic particle selection implemented in EMAN2 or manual particle selection implemented in EMAN1
CTF correctionSoftware - Name: CTFFIND (ver. 3)
Startup modelType 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 assignmentType: PROJECTION MATCHING / Software - Name: EMAN (ver. 1.9)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: Xmipp (ver. 2.4)
Final reconstructionApplied 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

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT

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