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- EMDB-2087: Structures from COPI-coated vesicles: single two-corner connection -

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Basic information

Entry
Database: EMDB / ID: 2087
TitleStructures from COPI-coated vesicles: single two-corner connection
Map dataReconstruction of a single two-corner connection
Samplesingle two-corner connection:
liposome membrane / Coatomer complex / Arf1
KeywordsCOPI-coated vesicles / subtomogram averaging / membrane trafficking / protein coat / coatomer / COPI
Sourceunidentified (others) / Mus musculus (house mouse) / Saccharomyces cerevisiae (baker's yeast)
Methodsubtomogram averaging / cryo EM / 38 Å resolution
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
DateDeposition: Apr 20, 2012 / Header (metadata) release: May 24, 2012 / Map release: May 25, 2012 / Last update: Aug 29, 2012

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.524
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.524
  • 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_2087.map.gz (map file in CCP4 format, 10720 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
140 pix
4.94 Å/pix.
= 691.6 Å
140 pix
4.94 Å/pix.
= 691.6 Å
140 pix
4.94 Å/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
Contour Level:0.524 (by author), 0.524 (movie #1):
Minimum - Maximum0E-8 - 1.00000000
Average (Standard dev.)0.35027605 (0.08127932)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions140140140
Origin000
Limit139139139
Spacing140140140
CellA=B=C: 691.60004 Å
α=β=γ: 90.0 deg.

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/mean0.0001.0000.350

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Supplemental data

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Sample components

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Entire single two-corner connection

EntireName: single two-corner connection / Number of components: 3

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Component #1: cellular-component, liposome membrane

Cellular-componentName: liposome membrane / Recombinant expression: No
SourceSpecies: unidentified (others)

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Component #2: protein, Coatomer complex

ProteinName: Coatomer complex / a.k.a: COPI / Recombinant expression: Yes
MassTheoretical: 560 kDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: unidentified baculovirus

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Component #3: protein, Arf1

ProteinName: Arf1 / Recombinant expression: Yes
MassTheoretical: 20 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenMethod: cryo EM
Sample solutionBuffer solution: 50mM Hepes , 50 mM KOAc, 1 mM MgCl2 / pH: 7.5
Support film300 mesh copper grid with holey carbon support, glow discharged
VitrificationInstrument: OTHER / Cryogen name: ETHANE / Temperature: 90 K / Humidity: 100 % / Method: Hand plunging

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300 / Date: May 6, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 60 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 27500 X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 2300 - 4300 nm / Energy filter: Gatan GIF 2000
Specimen HolderModel: GATAN LIQUID NITROGEN / Tilt Angle: -60 - 60 deg. / Temperature: K ( 90 - K)
CameraDetector: GENERIC CCD

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Image acquisition

Image acquisitionBit depth: 14

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Image processing

ProcessingMethod: subtomogram averaging
Details: CTF correction was performed. Average number of tilts used in the 3D reconstructions: 41. Average tomographic tilt angle increment: 3.
3D reconstructionAlgorithm: subtomogram averaging / Software: IMOD, TOM, package, Matlab / CTF correction: CTF multiplication / Resolution: 38 Å
Resolution method: FSC at 0.5 cut-off, independently processed datasets, gold-standard

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