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- EMDB-2431: The structure of the COPII coat assembled on membranes -

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Basic information

Entry
Database: EMDB / ID: EMD-2431
TitleThe structure of the COPII coat assembled on membranes
Map dataSec13/31 complex (as part of complete coat assembled on membrane). Edge, right handed direction
Sample
  • Sample: Sec13/31 complex (as part of complete COPII assembled on membrane) edge in right-handed direction
  • Protein or peptide: Sec31
  • Protein or peptide: Sec13
KeywordsCOPII / coat / secretion / trafficking / Sec13 / Sec31
Function / homology
Function and homology information


Seh1-associated complex / positive regulation of ER to Golgi vesicle-mediated transport / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / COPII-mediated vesicle transport / nuclear pore localization / COPII-coated vesicle cargo loading / regulation of TORC1 signaling / nuclear pore outer ring / COPII vesicle coat ...Seh1-associated complex / positive regulation of ER to Golgi vesicle-mediated transport / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / COPII-mediated vesicle transport / nuclear pore localization / COPII-coated vesicle cargo loading / regulation of TORC1 signaling / nuclear pore outer ring / COPII vesicle coat / positive regulation of protein exit from endoplasmic reticulum / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / SUMOylation of SUMOylation proteins / mating projection tip / SUMOylation of RNA binding proteins / endoplasmic reticulum organization / SUMOylation of chromatin organization proteins / nucleocytoplasmic transport / vacuolar membrane / endoplasmic reticulum exit site / positive regulation of TOR signaling / mRNA transport / nuclear pore / ERAD pathway / positive regulation of TORC1 signaling / cell periphery / protein import into nucleus / protein transport / nuclear envelope / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / structural molecule activity / endoplasmic reticulum
Similarity search - Function
Protein transport protein SEC31 / Protein transport protein SEC31 / Protein transport protein SEC31-like / SRA1/Sec31 / Steroid receptor RNA activator (SRA1) / Ancestral coatomer element 1, Sec16/Sec31 / Sec23-binding domain of Sec16 / Sec13/Seh1 family / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. ...Protein transport protein SEC31 / Protein transport protein SEC31 / Protein transport protein SEC31-like / SRA1/Sec31 / Steroid receptor RNA activator (SRA1) / Ancestral coatomer element 1, Sec16/Sec31 / Sec23-binding domain of Sec16 / Sec13/Seh1 family / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
: / : / Protein transport protein SEC31 / Protein transport protein SEC13
Similarity search - Component
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
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4bzk
  • Surface level: 2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2431.png

Downloads & links

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Map

FileDownload / File: emd_2431.map.gz / Format: CCP4 / Size: 1.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSec13/31 complex (as part of complete coat assembled on membrane). Edge, right handed direction
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.3 Å/pix.
x 72 pix.
= 309.6 Å		4.3 Å/pix.
x 72 pix.
= 309.6 Å		4.3 Å/pix.
x 72 pix.
= 309.6 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: 2.0 / Movie #1: 2
Minimum - Maximum-2.49198461 - 6.59203815
Average (Standard dev.)0.0 (±0.99999869)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions727272
Spacing727272
CellA=B=C: 309.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.34.34.3
M x/y/z727272
origin x/y/z0.0000.0000.000
length x/y/z309.600309.600309.600
α/β/γ90.00090.00090.000
start NX/NY/NZ00-40
NX/NY/NZ555581
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS727272
D min/max/mean-2.4926.592-0.000

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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) edge in right-handed direction
Components
  • Sample: Sec13/31 complex (as part of complete COPII assembled on membrane) edge in right-handed direction
  • 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) edge in right-handed direction
type: sample / ID: 1000 / Oligomeric state: heterotetramers of sec13 and sec31 / 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: 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: 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 / Number subtomograms used: 192
CTF correctionDetails: each tilted image within tomogram
Final angle assignmentDetails: 0 0 0 in zyz convention

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Atomic model buiding 1

Initial modelPDB ID:

2pm6

SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation
Output model

PDB-4bzk:
The structure of the COPII coat assembled on membranes

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Atomic model buiding 2

Initial modelPDB ID:

2pm9

SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation
Output model

PDB-4bzk:
The structure of the COPII coat assembled on membranes

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