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- EMDB-4145: Subtomogram average of the ER membrane-associated ribosome from F... -

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Basic information

Entry
Database: EMDB / ID: 4145
TitleSubtomogram average of the ER membrane-associated ribosome from FIB-milled C. reinhardtii cells
SampleER membrane-associated ribosome from FIB-milled C. reinhardtii cells
SourceChlamydomonas reinhardtii / plant
Map dataSubtomogram average of the ER membrane-associated ribosome from FIB-milled C. reinhardtii cells
Methodsubtomogram averaging, at 19.4 A resolution
AuthorsPfeffer S / Schaffer M / Albert S / Engel BD / 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: 2
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 2
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_4145.map.gz (map file in CCP4 format, 28312 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
192 pix
3.42 A/pix
= 656.64 A
192 pix
3.42 A/pix
= 656.64 A
192 pix
3.42 A/pix
= 656.64 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 3.42 A
Density
Contour Level:2 (by author), 2 (movie #1):
Minimum - Maximum-12.472282 - 15.797783
Average (Standard dev.)-4.740255E-9 (0.99999994)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions192192192
Origin000
Limit191191191
Spacing192192192
CellA=B=C: 656.64 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z3.423.423.42
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z656.640656.640656.640
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-12.47215.798-0.000

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Supplemental data

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Sample components

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Entire ER membrane-associated ribosome from FIB-milled C. reinhardtii cells

EntireName: ER membrane-associated ribosome from FIB-milled C. reinhardtii cells
Number of components: 1

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Component #1: protein, ER membrane-associated ribosome from FIB-milled C. reinh...

ProteinName: ER membrane-associated ribosome from FIB-milled C. reinhardtii cells
Recombinant expression: No
SourceSpecies: Chlamydomonas reinhardtii / plant

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Experimental details

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Sample preparation

Specimen statecell
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 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: 19.4 A / Resolution method: FSC 0.5 CUT-OFF

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