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- EMDB-6228: Human apo-TRiC -

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Basic information

Entry
Database: EMDB / ID: EMD-6228
TitleHuman apo-TRiC
Map dataHuman apo-TRiC group I
Sample
  • Sample: Human apo-TRiC (sub-group I)
  • Protein or peptide: TCP-1 Ring Complex
Keywordseukaryotic chaperonin
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 20.0 Å
AuthorsRoh SH / Kasembeli M / Montoya JG / Trnka M / Lau WC / Burlingame A / Chiu W / Tweardy DJ
CitationJournal: Biophys J / Year: 2016
Title: Chaperonin TRiC/CCT Recognizes Fusion Oncoprotein AML1-ETO through Subunit-Specific Interactions.
Authors: Soung-Hun Roh / Moses M Kasembeli / Jesús G Galaz-Montoya / Wah Chiu / David J Tweardy /
Abstract: AML1-ETO is the translational product of a chimeric gene created by the stable chromosome translocation t (8;21)(q22;q22). It causes acute myeloid leukemia (AML) by dysregulating the expression of ...AML1-ETO is the translational product of a chimeric gene created by the stable chromosome translocation t (8;21)(q22;q22). It causes acute myeloid leukemia (AML) by dysregulating the expression of genes critical for myeloid cell development and differentiation and recently has been reported to bind multiple subunits of the mammalian cytosolic chaperonin TRiC (or CCT), primarily through its DNA binding domain (AML1-175). Through these interactions, TRiC plays an important role in the synthesis, folding, and activity of AML1-ETO. Using single-particle cryo-electron microscopy, we demonstrate here that a folding intermediate of AML1-ETO's DNA-binding domain (AML1-175) forms a stable complex with apo-TRiC. Our structure reveals that AML1-175 associates directly with a specific subset of TRiC subunits in the open conformation.
History
DepositionDec 30, 2014-
Header (metadata) releaseJan 21, 2015-
Map releaseMay 11, 2016-
UpdateMay 11, 2016-
Current statusMay 11, 2016Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6228.gif

Downloads & links

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Map

FileDownload / File: emd_6228.map.gz / Format: CCP4 / Size: 28.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman apo-TRiC group I
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.17 Å/pix.
x 196 pix.
= 425.32 Å		2.17 Å/pix.
x 196 pix.
= 425.32 Å		2.17 Å/pix.
x 196 pix.
= 425.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.17 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-0.72053909 - 2.46615744
Average (Standard dev.)0.0 (±0.24299312)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions196196196
Spacing196196196
CellA=B=C: 425.32 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.172.172.17
M x/y/z196196196
origin x/y/z0.0000.0000.000
length x/y/z425.320425.320425.320
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS196196196
D min/max/mean-0.7212.4660.000

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Supplemental data

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Sample components

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Entire : Human apo-TRiC (sub-group I)

EntireName: Human apo-TRiC (sub-group I)
Components
  • Sample: Human apo-TRiC (sub-group I)
  • Protein or peptide: TCP-1 Ring Complex

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Supramolecule #1000: Human apo-TRiC (sub-group I)

SupramoleculeName: Human apo-TRiC (sub-group I) / type: sample / ID: 1000 / Oligomeric state: 16 / Number unique components: 1
Molecular weightTheoretical: 1 MDa

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Macromolecule #1: TCP-1 Ring Complex

MacromoleculeName: TCP-1 Ring Complex / type: protein_or_peptide / ID: 1 / Name.synonym: TRiC, CCT / Oligomeric state: 16 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Cell: HeLa
Molecular weightTheoretical: 1 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.4
Details: 20 mM HEPES, pH 7.4, 5 mM MgCl2, 0.1 mM EDTA, 1 mM DTT, 2% glycerol, 1% PEG8000, 0.05% OG
GridDetails: 200 mesh Quantifoil holey carbon grid (1.2/1.3), acetone-washed and glow-discharged
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Instrument: LEICA EM GP / Method: Blot for 10 seconds from copper side of grid.

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Electron microscopy

MicroscopeJEOL 2010F
DateAug 14, 2013
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 2.17 µm / Number real images: 186 / Average electron dose: 25 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 69124 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: particle-based
Final reconstructionResolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: OTHER / Software - Name: EMAN2, Relion1.2 / Number images used: 8010

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