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- EMDB-1784: The Structure of a COPII Tubule -

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Basic information

Entry
Database: EMDB / ID: EMD-1784
TitleThe Structure of a COPII Tubule
Map dataThis is a raw Tomogram of a Sec1331 Tubule (suggested contour level 60.1)
Sample
  • Sample: Oligomeric assembly of Sec13-31
  • Protein or peptide: SEC13R
  • Protein or peptide: SEC31L1
KeywordsSecretory pathway / Cryo-electron microscopy / Cryo-electron tomography / COPII / cargo / Subvolume averaging
Function / homologyintracellular protein transport / WD40 repeat
Function and homology information
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM / Resolution: 85.0 Å
AuthorsODonnell J / Maddox K / Stagg S
CitationJournal: J Struct Biol / Year: 2011
Title: The structure of a COPII tubule.
Authors: Jason O'Donnell / Kerry Maddox / Scott Stagg /
Abstract: Nearly a third of all eukaryotic proteins are transported from the ER to the Golgi apparatus through the secretory pathway using COPII coated vesicles. Evidence suggests that this transport occurs ...Nearly a third of all eukaryotic proteins are transported from the ER to the Golgi apparatus through the secretory pathway using COPII coated vesicles. Evidence suggests that this transport occurs via 500-900 Å vesicles that bud from the ER membrane. It has been shown that procollagen molecules utilize the COPII proteins for transport, but it is unclear how the COPII coat can accommodate these ∼3000 Å long molecules. We now present a cryogenic electron tomographic reconstruction of a Sec13/31 tubule that is approximately 3300 Å long containing a hollow cylindrical interior that is 300 Å in diameter, dimensions that are consistent with those that are required to encapsulate a procollagen molecule wrapped in a membrane and accessory COPII components. This structure suggests a novel mechanism that the COPII coat may employ to transport elongated cargo.
History
DepositionSep 14, 2010-
Header (metadata) releaseSep 24, 2010-
Map releaseSep 24, 2010-
UpdateSep 9, 2011-
Current statusSep 9, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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  • Simplified surface model
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1784.jpg

Downloads & links

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Map

FileDownload / File: emd_1784.map.gz / Format: CCP4 / Size: 232.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a raw Tomogram of a Sec1331 Tubule (suggested contour level 60.1)
Voxel sizeX=Y=Z: 9.2 Å
Density
Contour LevelBy EMDB: 100.0
Minimum - Maximum-249.673000000000002 - 300.90100000000001
Average (Standard dev.)-1.21692 (±27.939399999999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500250
Spacing500500250
CellA: 4600 Å / B: 4600 Å / C: 2300 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z9.29.29.2
M x/y/z500500250
origin x/y/z0.0000.0000.000
length x/y/z4600.0004600.0002300.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS500500250
D min/max/mean-249.673300.901-1.217

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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: SEC13R
  • Protein or peptide: SEC31L1

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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 made by Interlocked Cuboctahedrons / Number unique components: 2
Molecular weightTheoretical: 8.1 MDa

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Macromolecule #1: SEC13R

MacromoleculeName: SEC13R / type: protein_or_peptide / ID: 1 / Name.synonym: Sec13 / Number of copies: 12 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Cell: Sf9
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceGO: intracellular protein transport / InterPro: WD40 repeat

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Macromolecule #2: SEC31L1

MacromoleculeName: SEC31L1 / type: protein_or_peptide / ID: 2 / Name.synonym: Sec31 / Number of copies: 12 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Cell: Sf9
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceGO: intracellular protein transport / InterPro: WD40 repeat

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography

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Sample preparation

BufferpH: 7.5
Details: 20 mM Tris-Cl, pH 7.5, 700 mM KOAc, 1mM MgOAc, 10mM DTT
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 5s with Gatan Solarus 950 plasma cleaner using a ratio of 75-25 of Argon and Oxygen respectively.
Method: Temperature of chamber was 4 degrees C. 0 seconds drain time. Single blot. 0 mm offset. 3 ul sample applied to grid. Blot for 2.5 seconds before plunging.

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/T
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 64
Electron beamAcceleration voltage: 300 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 24000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: 0 ° / Tilt series - Axis1 - Max angle: 64 ° / Tilt series - Axis1 - Angle increment: 2 °

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Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 85.0 Å / Resolution method: OTHER / Software - Name: PROTOMO / Number images used: 250
CTF correctionDetails: Phase correction for each image

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