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- EMDB-3183: Localized reconstruction of Sec13/31 vertex from dodecahedral COP... -

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Basic information

Entry
Database: EMDB / ID: EMD-3183
TitleLocalized reconstruction of Sec13/31 vertex from dodecahedral COPII cage
Map dataLocalized reconstrucion of COPII sec13/31 vertex calculated from data published by Stagg et al. (2006)
Sample
  • Sample: Oligomeric assembly of Sec13-31
  • Protein or peptide: Sec31
  • Protein or peptide: Sec13
KeywordsCOPII / vertex / sec13 / sec31
Function / homologyCOPII vesicle coat / intracellular protein transport / WD40 repeat
Function and homology information
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 14.0 Å
AuthorsIlca S / Kotecha A / Sun X / Poranen MP / Stuart DI / Huiskonen JT
CitationJournal: Nature / Year: 2006
Title: Structure of the Sec13/31 COPII coat cage.
Authors: Scott M Stagg / Cemal Gürkan / Douglas M Fowler / Paul LaPointe / Ted R Foss / Clinton S Potter / Bridget Carragher / William E Balch /
Abstract: Endomembranes of eukaryotic cells are dynamic structures that are in continuous communication through the activity of specialized cellular machineries, such as the coat protein complex II (COPII), ...Endomembranes of eukaryotic cells are dynamic structures that are in continuous communication through the activity of specialized cellular machineries, such as the coat protein complex II (COPII), which mediates cargo export from the endoplasmic reticulum (ER). COPII consists of the Sar1 GTPase, Sec23 and Sec24 (Sec23/24), where Sec23 is a Sar1-specific GTPase-activating protein and Sec24 functions in cargo selection, and Sec13 and Sec31 (Sec13/31), which has a structural role. Whereas recent results have shown that Sec23/24 and Sec13/31 can self-assemble to form COPII cage-like particles, we now show that Sec13/31 can self-assemble to form minimal cages in the absence of Sec23/24. We present a three-dimensional reconstruction of these Sec13/31 cages at 30 A resolution using cryo-electron microscopy and single particle analysis. These results reveal a novel cuboctahedron geometry with the potential to form a flexible lattice and to generate a diverse range of containers. Our data are consistent with a model for COPII coat complex assembly in which Sec23/24 has a non-structural role as a multivalent ligand localizing the self-assembly of Sec13/31 to form a cage lattice driving ER cargo export.
History
DepositionOct 3, 2015-
Header (metadata) releaseOct 28, 2015-
Map releaseNov 4, 2015-
UpdateFeb 17, 2016-
Current statusFeb 17, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.08
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-3183.jpg

emd_3183.jpg

Downloads & links

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Map

FileDownload / File: emd_3183.map.gz / Format: CCP4 / Size: 6.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocalized reconstrucion of COPII sec13/31 vertex calculated from data published by Stagg et al. (2006)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.78 Å/pix.
x 120 pix.
= 333.6 Å		2.78 Å/pix.
x 120 pix.
= 333.6 Å		2.78 Å/pix.
x 120 pix.
= 333.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.78 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08 / Movie #1: 0.08
Minimum - Maximum-0.03152725 - 0.18658105
Average (Standard dev.)0.00617628 (±0.01772222)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions120120120
Spacing120120120
CellA=B=C: 333.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.782.782.78
M x/y/z120120120
origin x/y/z0.0000.0000.000
length x/y/z333.600333.600333.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS120120120
D min/max/mean-0.0320.1870.006

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Supplemental data

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Segmentation: Mask used for FSC

AnnotationMask used for FSC
Fileemd_3183_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Oligomeric assembly of Sec13-31

EntireName: Oligomeric assembly of Sec13-31
Components
  • Sample: Oligomeric assembly of Sec13-31
  • Protein or peptide: Sec31
  • Protein or peptide: Sec13

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Supramolecule #1000: Oligomeric assembly of Sec13-31

SupramoleculeName: Oligomeric assembly of Sec13-31 / type: sample / ID: 1000
Oligomeric state: 24-mer of Sec13-31 heterotetramers forming a cuboctahedron
Number unique components: 2
Molecular weightExperimental: 8.14 MDa

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Macromolecule #1: Sec31

MacromoleculeName: Sec31 / type: protein_or_peptide / ID: 1 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Molecular weightExperimental: 139 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper) / Recombinant plasmid: pFastBac
SequenceGO: COPII vesicle coat / InterPro: WD40 repeat

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Macromolecule #2: Sec13

MacromoleculeName: Sec13 / type: protein_or_peptide / ID: 2 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Molecular weightExperimental: 33 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper) / Recombinant plasmid: pFastBac
SequenceGO: intracellular protein transport / InterPro: WD40 repeat

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.90 mg/mL
BufferpH: 6.5 / Details: 50mM MES pH 6.5, 225mM KOAc, 1mM MgCl2
GridDetails: Quantifoil 2/2, 400 mesh copper grid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: OTHER
Details: Vitrification instrument: FEI Vitrobot. Grid plasma cleaned for 30s with Fischione 1020 plasma cleaner using 75-25 Argon-Oxygen mix.
Method: Temperature of chamber was 4 degrees C. 0 seconds drain time. Single blot. 0 mm offset. 4 ul sample applied to grid. Blot for 3.0 seconds before plunging.

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Electron microscopy

MicroscopeFEI TECNAI 20
DateJan 1, 2006
Image recordingCategory: CCD / Film or detector model: OTHER / Number real images: 810 / Average electron dose: 20 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50360 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 6.6 µm / Nominal defocus min: 3.4 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsThe best particles were selected by 2D and 3D classification and then refined
CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 14.0 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 12663
FSC plot (resolution estimation)

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