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- EMDB-2085: Structures from COPI-coated vesicles: three-corner connection -

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Basic information

Entry
Database: EMDB / ID: EMD-2085
TitleStructures from COPI-coated vesicles: three-corner connection
Map dataReconstruction of a three-corner connection
Sample
  • Sample: three-corner connection
  • Organelle or cellular component: liposome membrane
  • Protein or peptide: Coatomer complex
  • Protein or peptide: Arf1
KeywordsCOPI-coated vesicles / subtomogram averaging / membrane trafficking / protein coat / coatomer / COPI
Biological speciesunidentified (others) / Mus musculus (house mouse) / Saccharomyces cerevisiae (brewer's yeast)
Methodsubtomogram averaging / cryo EM / Resolution: 32.0 Å
AuthorsFaini M / Prinz S / Beck R / Schorb M / Riches JD / Bacia K / Brugger B / Wieland FT / Briggs JAG
CitationJournal: Science / Year: 2012
Title: The structures of COPI-coated vesicles reveal alternate coatomer conformations and interactions.
Authors: Marco Faini / Simone Prinz / Rainer Beck / Martin Schorb / James D Riches / Kirsten Bacia / Britta Brügger / Felix T Wieland / John A G Briggs /
Abstract: Transport between compartments of eukaryotic cells is mediated by coated vesicles. The archetypal protein coats COPI, COPII, and clathrin are conserved from yeast to human. Structural studies of ...Transport between compartments of eukaryotic cells is mediated by coated vesicles. The archetypal protein coats COPI, COPII, and clathrin are conserved from yeast to human. Structural studies of COPII and clathrin coats assembled in vitro without membranes suggest that coat components assemble regular cages with the same set of interactions between components. Detailed three-dimensional structures of coated membrane vesicles have not been obtained. Here, we solved the structures of individual COPI-coated membrane vesicles by cryoelectron tomography and subtomogram averaging of in vitro reconstituted budding reactions. The coat protein complex, coatomer, was observed to adopt alternative conformations to change the number of other coatomers with which it interacts and to form vesicles with variable sizes and shapes. This represents a fundamentally different basis for vesicle coat assembly.
History
DepositionApr 20, 2012-
Header (metadata) releaseMay 24, 2012-
Map releaseMay 25, 2012-
UpdateAug 29, 2012-
Current statusAug 29, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.494
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.494
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2085.tif

Downloads & links

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Map

FileDownload / File: emd_2085.map.gz / Format: CCP4 / Size: 10.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of a three-corner connection
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.94 Å/pix.
x 140 pix.
= 691.6 Å		4.94 Å/pix.
x 140 pix.
= 691.6 Å		4.94 Å/pix.
x 140 pix.
= 691.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.494 / Movie #1: 0.494
Minimum - Maximum0.0 - 1.0
Average (Standard dev.)0.32255161 (±0.09545103)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions140140140
Spacing140140140
CellA=B=C: 691.60004 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.944.944.94
M x/y/z140140140
origin x/y/z0.0000.0000.000
length x/y/z691.600691.600691.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ128128168
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS140140140
D min/max/mean0.0001.0000.323

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Supplemental data

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Sample components

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Entire : three-corner connection

EntireName: three-corner connection
Components
  • Sample: three-corner connection
  • Organelle or cellular component: liposome membrane
  • Protein or peptide: Coatomer complex
  • Protein or peptide: Arf1

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Supramolecule #1000: three-corner connection

SupramoleculeName: three-corner connection / type: sample / ID: 1000 / Number unique components: 3

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Supramolecule #1: liposome membrane

SupramoleculeName: liposome membrane / type: organelle_or_cellular_component / ID: 1 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: unidentified (others)

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Macromolecule #1: Coatomer complex

MacromoleculeName: Coatomer complex / type: protein_or_peptide / ID: 1 / Name.synonym: COPI / Recombinant expression: Yes
Source (natural)Organism: Mus musculus (house mouse) / synonym: Mouse
Molecular weightTheoretical: 560 KDa
Recombinant expressionOrganism: unidentified baculovirus

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Macromolecule #2: Arf1

MacromoleculeName: Arf1 / type: protein_or_peptide / ID: 2 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's Yeast
Molecular weightTheoretical: 20 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging

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Sample preparation

BufferpH: 7.5 / Details: 50mM Hepes , 50 mM KOAc, 1 mM MgCl2
GridDetails: 300 mesh copper grid with holey carbon support, glow discharged
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 90 K / Instrument: OTHER / Method: Hand plunging

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Electron microscopy

MicroscopeFEI POLARA 300
TemperatureMin: 90 K
Specialist opticsEnergy filter - Name: Gatan GIF 2000
DateMay 6, 2011
Image recordingCategory: CCD / Film or detector model: GENERIC CCD / Average electron dose: 60 e/Å2 / Bits/pixel: 14
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 4.3 µm / Nominal defocus min: 2.3 µm / Nominal magnification: 27500
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 °
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

DetailsCTF correction was performed. Average number of tilts used in the 3D reconstructions: 41. Average tomographic tilt angle increment: 3.
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 32.0 Å / Resolution method: OTHER / Software - Name: IMOD, TOM, package, Matlab
CTF correctionDetails: CTF multiplication

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