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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: 4143
TitleSubtomogram average of the ER membrane-associated ribosome from human TRAPdelta-deficient fibroblasts
SampleER membrane-associated ribosome from human TRAPdelta-deficient fibroblasts
SourceHomo sapiens / human
Map dataSubtomogram average of the ER membrane-associated ribosome from human TRAPdelta-deficient fibroblasts
Methodsubtomogram averaging, at 14.9 A resolution
AuthorsPfeffer S / Dudek J / Ng BG / Zimmermann R / Freeze HH / Foerster F
CitationNat Commun, 2017, 8, 14516-14516

Nat Commun, 2017, 8, 14516-14516 StrPapers
Dissecting the molecular organization of the translocon-associated protein complex.
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

DateDeposition: Oct 13, 2016 / Header (metadata) release: Oct 26, 2016 / Map release: Mar 1, 2017 / Last update: Oct 13, 2016

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.5
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 1.5
  • Imaged by UCSF CHIMERA
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Supplemental images

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Map

Fileemd_4143.map.gz (map file in CCP4 format, 42593 KB)
Projections & slices

Image control

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

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.62 A
Density
Contour Level:1.5 (by author), 1.5 (movie #1):
Minimum - Maximum-10.98011 - 13.124097
Average (Standard dev.)1.338255E-9 (0.99999994)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions220220220
Origin000
Limit219219219
Spacing220220220
CellA=B=C: 576.39996 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
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
Number of components: 1

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Component #1: protein, ER membrane-associated ribosome from human TRAPdelta-def...

ProteinName: ER membrane-associated ribosome from human TRAPdelta-deficient fibroblasts
Recombinant expression: No
SourceSpecies: Homo sapiens / human

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE MIXTURE

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Electron microscopy imaging

ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.5 e/A2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C1 (asymmetric)
3D reconstructionSoftware: PyTom / Resolution: 14.9 A / Resolution method: FSC 0.5 CUT-OFF

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