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- EMDB-3971: The in situ structure of the Chlamydomonas COPI coat: average fro... -

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Basic information

Entry
Database: EMDB / ID: 3971
TitleThe in situ structure of the Chlamydomonas COPI coat: average from the cis-Golgi region
Map dataThe in situ structure of the Chlamydomonas COPI coat derived from the cis Golgi region
SampleWhole Chlamydomonas cells:
SourceChlamydomonas reinhardtii (plant)
Methodsubtomogram averaging / cryo EM / 24 Å resolution
AuthorsBykov YS / Schaffer M / Dodonova SO / Albert S / Plitzko JM / Baumeister W / Engel BD / Briggs JAG
CitationJournal: Elife / Year: 2017
Title: The structure of the COPI coat determined within the cell.
Authors: Yury S Bykov / Miroslava Schaffer / Svetlana O Dodonova / Sahradha Albert / Jürgen M Plitzko / Wolfgang Baumeister / Benjamin D Engel / John Ag Briggs
DateDeposition: Nov 7, 2017 / Header (metadata) release: Nov 15, 2017 / Map release: Nov 29, 2017 / Last update: Nov 29, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3971.map.gz (map file in CCP4 format, 8389 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
128 pix
3.42 Å/pix.
= 437.76 Å
128 pix
3.42 Å/pix.
= 437.76 Å
128 pix
3.42 Å/pix.
= 437.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.42 Å
Density
Contour Level:0.1 (by author), 0.1 (movie #1):
Minimum - Maximum-0.18736187 - 0.3396858
Average (Standard dev.)0.009714867 (0.08686227)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions128128128
Origin0.00.00.0
Limit127.0127.0127.0
Spacing128128128
CellA=B=C: 437.76 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.423.423.42
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z437.760437.760437.760
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.1870.3400.010

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Supplemental data

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Sample components

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Entire Whole Chlamydomonas cells

EntireName: Whole Chlamydomonas cells
Details: Grown suspended in TAP media, with normal atmosphere aeration and constant light
Number of components: 1

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Component #1: cellular-component, Whole Chlamydomonas cells

Cellular-componentName: Whole Chlamydomonas cells
Details: Grown suspended in TAP media, with normal atmosphere aeration and constant light
Recombinant expression: No
SourceSpecies: Chlamydomonas reinhardtii (plant) / Strain: mat3-4
Source (natural)Organelle: Golgi

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Experimental details

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Sample preparation

SpecimenSpecimen state: cell / Method: cryo EM
Sample solutionBuffer solution: TAP media / pH: 7
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: OTHER / Humidity: 90 %
Details: Blotted from the back side for 10 seconds with 10 blot force before plunging.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.5 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 42000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 4000.0 - 6000.0 nm / Energy filter: GIF Quantum LS / Energy window: 0-20 eV
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C3 (3 fold cyclic) / Number of subtomograms: 897
3D reconstructionAlgorithm: BACK PROJECTION / Software: TOM, AV3 / Resolution: 24 Å / Resolution method: FSC 0.143 CUT-OFF
Details: Only subtomograms contained in buds and vesicles of the cis-Golgi region were used to generate this average. No additional alignment was performed.

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Atomic model buiding

Modeling #1Refinement protocol: rigid body

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