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- EMDB-4143: Subtomogram average of the ER membrane-associated ribosome from h... -

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Basic information

Entry
Database: EMDB / ID: EMD-4143
TitleSubtomogram average of the ER membrane-associated ribosome from human TRAPdelta-deficient fibroblasts
Map dataSubtomogram average of the ER membrane-associated ribosome from human TRAPdelta-deficient fibroblasts
Sample
  • Complex: ER membrane-associated ribosome from human TRAPdelta-deficient fibroblasts
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 14.9 Å
AuthorsPfeffer S / Dudek J / Ng BG / Zimmermann R / Freeze HH / Foerster F
CitationJournal: Nat Commun / Year: 2017
Title: Dissecting the molecular organization of the translocon-associated protein complex.
Authors: Stefan Pfeffer / Johanna Dudek / Miroslava Schaffer / Bobby G Ng / Sahradha Albert / Jürgen M Plitzko / Wolfgang Baumeister / Richard Zimmermann / Hudson H Freeze / Benjamin D Engel / Friedrich Förster /
Abstract: In eukaryotic cells, one-third of all proteins must be transported across or inserted into the endoplasmic reticulum (ER) membrane by the ER protein translocon. The translocon-associated protein ...In eukaryotic cells, one-third of all proteins must be transported across or inserted into the endoplasmic reticulum (ER) membrane by the ER protein translocon. The translocon-associated protein (TRAP) complex is an integral component of the translocon, assisting the Sec61 protein-conducting channel by regulating signal sequence and transmembrane helix insertion in a substrate-dependent manner. Here we use cryo-electron tomography (CET) to study the structure of the native translocon in evolutionarily divergent organisms and disease-linked TRAP mutant fibroblasts from human patients. The structural differences detected by subtomogram analysis form a basis for dissecting the molecular organization of the TRAP complex. We assign positions to the four TRAP subunits within the complex, providing insights into their individual functions. The revealed molecular architecture of a central translocon component advances our understanding of membrane protein biogenesis and sheds light on the role of TRAP in human congenital disorders of glycosylation.
History
DepositionOct 13, 2016-
Header (metadata) releaseOct 26, 2016-
Map releaseMar 1, 2017-
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: 1.5
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4143.png

Downloads & links

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Map

FileDownload / File: emd_4143.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of the ER membrane-associated ribosome from human TRAPdelta-deficient fibroblasts
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.62 Å/pix.
x 220 pix.
= 576.4 Å		2.62 Å/pix.
x 220 pix.
= 576.4 Å		2.62 Å/pix.
x 220 pix.
= 576.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.62 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5 / Movie #1: 1.5
Minimum - Maximum-10.98011 - 13.124097000000001
Average (Standard dev.)0.000000001338255 (±0.99999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 576.39996 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.622.622.62
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z576.400576.400576.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-10.98013.1240.000

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Supplemental data

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Sample components

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Entire : ER membrane-associated ribosome from human TRAPdelta-deficient fi...

EntireName: ER membrane-associated ribosome from human TRAPdelta-deficient fibroblasts
Components
  • Complex: ER membrane-associated ribosome from human TRAPdelta-deficient fibroblasts

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Supramolecule #1: ER membrane-associated ribosome from human TRAPdelta-deficient fi...

SupramoleculeName: ER membrane-associated ribosome from human TRAPdelta-deficient fibroblasts
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 14.9 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PyTom / Number subtomograms used: 2319
ExtractionNumber tomograms: 59 / Number images used: 5276
Final angle assignmentType: OTHER

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