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- EMDB-1786: The subvolume averaged map of a Sec13-31 Tubule -

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Basic information

Entry
Database: EMDB / ID: EMD-1786
TitleThe subvolume averaged map of a Sec13-31 Tubule
Map dataThis is a subvolume aveaged map corresponding to Sec13-31 tubule
Sample
  • Sample: Sec13-31 Tubule
  • 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)
Methodsubtomogram averaging / 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
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1786.jpg

Downloads & links

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Map

FileDownload / File: emd_1786.map.gz / Format: CCP4 / Size: 26.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a subvolume aveaged map corresponding to Sec13-31 tubule
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
9.2 Å/pix.
x 192 pix.
= 1766.4 Å		9.2 Å/pix.
x 192 pix.
= 1766.4 Å		9.2 Å/pix.
x 192 pix.
= 1766.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 9.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-2.04879 - 5.05841
Average (Standard dev.)0.00000000077868 (±0.289986)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-94-94-94
Dimensions192192192
Spacing192192192
CellA=B=C: 1766.4 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z9.29.29.2
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z1766.4001766.4001766.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-94-94-94
NC/NR/NS192192192
D min/max/mean-2.0495.0580.000

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Supplemental data

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Sample components

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Entire : Sec13-31 Tubule

EntireName: Sec13-31 Tubule
Components
  • Sample: Sec13-31 Tubule
  • Protein or peptide: SEC13R
  • Protein or peptide: SEC31L1

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Supramolecule #1000: Sec13-31 Tubule

SupramoleculeName: Sec13-31 Tubule / type: sample / ID: 1000 / 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
Processingsubtomogram averaging

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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 30s with Fischione 1020 plasma cleaner using a ratio of 75-25 of Argon to oxygen, respectively.
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 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 - Max angle: 64 °

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Image processing

DetailsThe subvolume motifs were selected by the program PROTOMO. Average number of tilts used in the 3D reconstructions: 250. Average tomographic tilt angle increment: 2.
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 85.0 Å / Resolution method: OTHER / Software - Name: PROTOMO
Details: The subvolume averaged Tubule was averaged from 8 motifs

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