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- EMDB-2429: The structure of the COPII coat assembled on membranes -

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Basic information

Entry
Database: EMDB / ID: EMD-2429
TitleThe structure of the COPII coat assembled on membranes
Map datasec31/13 outer COP2 coat layer vertex
Sample
  • Sample: Sec13/31 complex (as part of complete COPII assembled on membrane) cage vertex
  • Protein or peptide: Sec31
  • Protein or peptide: Sec13
KeywordsCOPII / coat / secretion / trafficking / Sec13 / Sec31
Function / homology: / :
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsubtomogram averaging / cryo EM / negative staining / Resolution: 40.0 Å
AuthorsZanetti G / Prinz S / Daum S / Meister A / Schekman R / Bacia K / Briggs JAG
CitationJournal: Elife / Year: 2013
Title: The structure of the COPII transport-vesicle coat assembled on membranes.
Authors: Giulia Zanetti / Simone Prinz / Sebastian Daum / Annette Meister / Randy Schekman / Kirsten Bacia / John A G Briggs /
Abstract: Coat protein complex II (COPII) mediates formation of the membrane vesicles that export newly synthesised proteins from the endoplasmic reticulum. The inner COPII proteins bind to cargo and membrane, ...Coat protein complex II (COPII) mediates formation of the membrane vesicles that export newly synthesised proteins from the endoplasmic reticulum. The inner COPII proteins bind to cargo and membrane, linking them to the outer COPII components that form a cage around the vesicle. Regulated flexibility in coat architecture is essential for transport of a variety of differently sized cargoes, but structural data on the assembled coat has not been available. We have used cryo-electron tomography and subtomogram averaging to determine the structure of the complete, membrane-assembled COPII coat. We describe a novel arrangement of the outer coat and find that the inner coat can assemble into regular lattices. The data reveal how coat subunits interact with one another and with the membrane, suggesting how coordinated assembly of inner and outer coats can mediate and regulate packaging of vesicles ranging from small spheres to large tubular carriers. DOI:http://dx.doi.org/10.7554/eLife.00951.001.
History
DepositionJul 26, 2013-
Header (metadata) releaseAug 7, 2013-
Map releaseSep 18, 2013-
UpdateOct 9, 2013-
Current statusOct 9, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2429.png

Downloads & links

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Map

FileDownload / File: emd_2429.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsec31/13 outer COP2 coat layer vertex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.3 Å/pix.
x 128 pix.
= 550.4 Å		4.3 Å/pix.
x 128 pix.
= 550.4 Å		4.3 Å/pix.
x 128 pix.
= 550.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.5 / Movie #1: 2.5
Minimum - Maximum-1.75932884 - 7.09553051
Average (Standard dev.)0.0 (±0.99999976)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 550.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.34.34.3
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z550.400550.400550.400
α/β/γ90.00090.00090.000
start NX/NY/NZ00-40
NX/NY/NZ555581
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-1.7597.096-0.000

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Supplemental data

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Sample components

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Entire : Sec13/31 complex (as part of complete COPII assembled on membrane...

EntireName: Sec13/31 complex (as part of complete COPII assembled on membrane) cage vertex
Components
  • Sample: Sec13/31 complex (as part of complete COPII assembled on membrane) cage vertex
  • Protein or peptide: Sec31
  • Protein or peptide: Sec13

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Supramolecule #1000: Sec13/31 complex (as part of complete COPII assembled on membrane...

SupramoleculeName: Sec13/31 complex (as part of complete COPII assembled on membrane) cage vertex
type: sample / ID: 1000 / Oligomeric state: 4 heterotetramers form a vertex / Number unique components: 2
Molecular weightExperimental: 319.236 KDa / Theoretical: 319.236 KDa

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Macromolecule #1: Sec31

MacromoleculeName: Sec31 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Oligomeric state: heterotetramer / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast / Location in cell: cytosol/endoplasmic reticulum
Molecular weightExperimental: 138.824 KDa / Theoretical: 138.824 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast) / Recombinant strain: RSY1112 / Recombinant plasmid: pNS3141 (6H31/CK1313)
SequenceUniProtKB: UNIPROTKB: E7Q1I6

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Macromolecule #2: Sec13

MacromoleculeName: Sec13 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Oligomeric state: heterotetramer / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast / Location in cell: cytosol/endoplasmic reticulum
Molecular weightExperimental: 20.79 KDa / Theoretical: 27.9 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast) / Recombinant strain: RSY1112 / Recombinant plasmid: pNS3141 (6H31/CK1313)
SequenceUniProtKB: UNIPROTKB: E7Q6Z3

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsubtomogram averaging
Aggregation statehelical array

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Sample preparation

Concentration0.03 mg/mL
BufferpH: 6.8 / Details: HEPES, 50 mM KOAc, 1.2 mM MgCl2
StainingType: NEGATIVE / Details: plunge frozen
GridDetails: C-flat grids
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy #1

Microscopy ID1
MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GATAN GIF 2002
DateSep 18, 2012
Image recordingCategory: CCD / Film or detector model: GATAN MULTISCAN / Number real images: 26 / Average electron dose: 80 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.2 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 19500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 °
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Electron microscopy #2

Microscopy ID2
MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GATAN GIF 2002
DateJun 19, 2012
Image recordingCategory: CCD / Film or detector model: GATAN MULTISCAN / Number real images: 26 / Average electron dose: 80 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.2 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 19500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 °
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Detailssee materials and methods in relevant publication
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 40.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: TOM/AV3, Matlab, dynamo / Number subtomograms used: 417
CTF correctionDetails: each tilted image within tomogram
Final angle assignmentDetails: 0 0 0 in zyz convention

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