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- EMDB-5532: Single particle tomography of TRiC chaperonin with internalized s... -

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Basic information

Entry
Database: EMDB / ID: EMD-5532
TitleSingle particle tomography of TRiC chaperonin with internalized substrate
Map dataSingle Particle Tomography average of TRiC chaperonin incubated with mhttQ51
Sample
  • Sample: TRiC chaperonin + mhttQ51
  • Protein or peptide: TCP-1 Ring Complex with mutant huntingtin Q51 exon-1
KeywordsMutant huntingtin / TRiC chaperonin / Single Particle Tomography / cryo electron microscopy / amyloid
Biological speciesBos taurus (cattle)
Methodsubtomogram averaging / cryo EM / Resolution: 50.0 Å
AuthorsShahmoradian SH / Galaz JG / Schmid MF / Cong Y / Ma B / Spiess C / Frydman J / Ludtke SJ / Chiu W
CitationJournal: Elife / Year: 2013
Title: TRiC's tricks inhibit huntingtin aggregation.
Authors: Sarah H Shahmoradian / Jesus G Galaz-Montoya / Michael F Schmid / Yao Cong / Boxue Ma / Christoph Spiess / Judith Frydman / Steven J Ludtke / Wah Chiu /
Abstract: In Huntington's disease, a mutated version of the huntingtin protein leads to cell death. Mutant huntingtin is known to aggregate, a process that can be inhibited by the eukaryotic chaperonin TRiC ...In Huntington's disease, a mutated version of the huntingtin protein leads to cell death. Mutant huntingtin is known to aggregate, a process that can be inhibited by the eukaryotic chaperonin TRiC (TCP1-ring complex) in vitro and in vivo. A structural understanding of the genesis of aggregates and their modulation by cellular chaperones could facilitate the development of therapies but has been hindered by the heterogeneity of amyloid aggregates. Using cryo-electron microscopy (cryoEM) and single particle cryo-electron tomography (SPT) we characterize the growth of fibrillar aggregates of mutant huntingtin exon 1 containing an expanded polyglutamine tract with 51 residues (mhttQ51), and resolve 3-D structures of the chaperonin TRiC interacting with mhttQ51. We find that TRiC caps mhttQ51 fibril tips via the apical domains of its subunits, and also encapsulates smaller mhtt oligomers within its chamber. These two complementary mechanisms provide a structural description for TRiC's inhibition of mhttQ51 aggregation in vitro. DOI:http://dx.doi.org/10.7554/eLife.00710.001.
History
DepositionDec 3, 2012-
Header (metadata) releaseDec 19, 2012-
Map releaseJul 17, 2013-
UpdateSep 25, 2013-
Current statusSep 25, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.425
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.425
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5532.png

emd_5532_1.png

Downloads & links

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Map

FileDownload / File: emd_5532.map.gz / Format: CCP4 / Size: 3.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSingle Particle Tomography average of TRiC chaperonin incubated with mhttQ51
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.4 Å/pix.
x 96 pix.
= 422.496 Å		4.4 Å/pix.
x 96 pix.
= 422.496 Å		4.4 Å/pix.
x 96 pix.
= 422.496 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.401 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.425 / Movie #1: 0.425
Minimum - Maximum-0.66890943 - 1.06296468
Average (Standard dev.)0.00280593 (±0.1433346)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions969696
Spacing969696
CellA=B=C: 422.496 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.4014.4014.401
M x/y/z969696
origin x/y/z0.0000.0000.000
length x/y/z422.496422.496422.496
α/β/γ90.00090.00090.000
start NX/NY/NZ-5029166
NX/NY/NZ106122134
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS969696
D min/max/mean-0.6691.0630.003

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Supplemental data

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Sample components

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Entire : TRiC chaperonin + mhttQ51

EntireName: TRiC chaperonin + mhttQ51
Components
  • Sample: TRiC chaperonin + mhttQ51
  • Protein or peptide: TCP-1 Ring Complex with mutant huntingtin Q51 exon-1

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Supramolecule #1000: TRiC chaperonin + mhttQ51

SupramoleculeName: TRiC chaperonin + mhttQ51 / type: sample / ID: 1000 / Number unique components: 2
Molecular weightTheoretical: 1.01 MDa

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Macromolecule #1: TCP-1 Ring Complex with mutant huntingtin Q51 exon-1

MacromoleculeName: TCP-1 Ring Complex with mutant huntingtin Q51 exon-1 / type: protein_or_peptide / ID: 1 / Name.synonym: TRiC with mhtt / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Bos taurus (cattle) / synonym: bovine / Tissue: Testis
Molecular weightTheoretical: 1.01 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

GridDetails: 200 mesh copper Quantifoil grid, glow discharged
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeJEOL 2100
DetailsSerial EM software
DateMar 19, 2009
Image recordingCategory: CCD / Film or detector model: GENERIC CCD / Digitization - Sampling interval: 2 µm / Number real images: 121 / Average electron dose: 62 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 5.0 µm / Nominal magnification: 25000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 °

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 50.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN2 / Number subtomograms used: 7
Final 3D classificationNumber classes: 1

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