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- EMDB-1232: Structure of the Sec13-31 COPII coat cage. -

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Basic information

Entry
Database: EMDB / ID: EMD-1232
TitleStructure of the Sec13-31 COPII coat cage.
Map dataThis is a 30 angstrom resolution map of the self-assembing Sec13/31 cage.
Sample
  • Sample: Oligomeric assembly of Sec13-31
  • Protein or peptide: Sec13
  • Protein or peptide: Sec31
Function / homologyCOPII vesicle coat / intracellular protein transport / WD40 repeat
Function and homology information
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 30.0 Å
AuthorsStagg SM / Gurkan C / Fowler DM / LaPointe P / Foss TR / Potter CS / Carragher B / Balch WE
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
DepositionMay 26, 2006-
Header (metadata) releaseJun 5, 2006-
Map releaseJun 5, 2006-
UpdateJul 22, 2011-
Current statusJul 22, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 3.3
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1232.gif

EMD-1232.png

Downloads & links

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Map

FileDownload / File: emd_1232.map.gz / Format: CCP4 / Size: 26.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a 30 angstrom resolution map of the self-assembing Sec13/31 cage.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.53 Å/pix.
x 192 pix.
= 868.992 Å		4.53 Å/pix.
x 192 pix.
= 868.992 Å		4.53 Å/pix.
x 192 pix.
= 868.992 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.526 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 5.0 / Movie #1: 3.3
Minimum - Maximum-6.01866 - 12.2407
Average (Standard dev.)0.00000000139742 (±0.928711)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-96-96-96
Dimensions192192192
Spacing192192192
CellA=B=C: 868.992 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.5264.5264.526
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z868.992868.992868.992
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS-96-96-96
NC/NR/NS192192192
D min/max/mean-6.01912.2410.000

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Supplemental data

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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: Sec13
  • Protein or peptide: Sec31

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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 weightTheoretical: 8.14 MDa

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Macromolecule #1: Sec13

MacromoleculeName: Sec13 / type: protein_or_peptide / ID: 1 / Name.synonym: Sec13 / Details: SEC13R / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Molecular weightExperimental: 33 MDa / Theoretical: 33 MDa
Recombinant expressionOrganism: Baculovirus infected Tn5 insect cells / Recombinant plasmid: pFastBac
SequenceGO: intracellular protein transport / InterPro: WD40 repeat

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Macromolecule #2: Sec31

MacromoleculeName: Sec31 / type: protein_or_peptide / ID: 2 / Name.synonym: Sec31 / Details: SEC31L1 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Molecular weightExperimental: 139 MDa / Theoretical: 139 MDa
Recombinant expressionOrganism: Baculovirus infected Tn5 insect cells / Recombinant plasmid: pFastBac
SequenceGO: COPII vesicle coat / 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

Concentration0.9 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 % / Chamber temperature: 93 K / 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
TemperatureAverage: 94 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 50,000X magnification
DateFeb 2, 2005
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 20 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 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder.
Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsThe images were acquired using the Leginon automated data aquisition system. The particles were automatically selected using the Selexon package. The CTF was automatically estimated using the ACE package
CTF correctionDetails: Phase correction for each particle.
Final reconstructionApplied symmetry - Point group: O (octahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 9777
Final two d classificationNumber classes: 92

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