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- EMDB-1511: COPII coat -

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Basic information

Entry
Database: EMDB / ID: EMD-1511
TitleCOPII coat
Map dataThis is a reconstruction of a COPII coat comprised of Sec13-31 and Sec23-24.
Sample
  • Sample: Sec13/31 bound to Sec23/24
  • Organelle or cellular component: COPII coat
Keywordsvesicle trafficking / COPII / icosidodecahedron / secretory pathway / endoplasmic reticulum / automation
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 43.0 Å
AuthorsStagg SM / LaPointe P / Razvi A / Gurkan C / Potter CS / Carragher B / Balch WE
CitationJournal: Cell / Year: 2008
Title: Structural basis for cargo regulation of COPII coat assembly.
Authors: Scott M Stagg / Paul LaPointe / Abbas Razvi / Cemal Gürkan / Clinton S Potter / Bridget Carragher / William E Balch /
Abstract: Using cryo-electron microscopy, we have solved the structure of an icosidodecahedral COPII coat involved in cargo export from the endoplasmic reticulum (ER) coassembled from purified cargo adaptor ...Using cryo-electron microscopy, we have solved the structure of an icosidodecahedral COPII coat involved in cargo export from the endoplasmic reticulum (ER) coassembled from purified cargo adaptor Sec23-24 and Sec13-31 lattice-forming complexes. The coat structure shows a tetrameric assembly of the Sec23-24 adaptor layer that is well positioned beneath the vertices and edges of the Sec13-31 lattice. Fitting the known crystal structures of the COPII proteins into the density map reveals a flexible hinge region stemming from interactions between WD40 beta-propeller domains present in Sec13 and Sec31 at the vertices. The structure shows that the hinge region can direct geometric cage expansion to accommodate a wide range of bulky cargo, including procollagen and chylomicrons, that is sensitive to adaptor function in inherited disease. The COPII coat structure leads us to propose a mechanism by which cargo drives cage assembly and membrane curvature for budding from the ER.
History
DepositionMay 24, 2008-
Header (metadata) releaseMay 27, 2008-
Map releaseMar 31, 2009-
UpdateMar 31, 2009-
Current statusMar 31, 2009Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2.2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1511.gif

Downloads & links

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Map

FileDownload / File: emd_1511.map.gz / Format: CCP4 / Size: 26.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a reconstruction of a COPII coat comprised of Sec13-31 and Sec23-24.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.7 Å/pix.
x 192 pix.
= 1478.4 Å		7.7 Å/pix.
x 192 pix.
= 1478.4 Å		7.7 Å/pix.
x 192 pix.
= 1478.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 7.7 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 2.04 / Movie #1: 2.2
Minimum - Maximum-4.13365 - 10.414899999999999
Average (Standard dev.)-0.0000000101831 (±0.939892)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-96-96-96
Dimensions192192192
Spacing192192192
CellA=B=C: 1478.4 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.77.77.7
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z1478.4001478.4001478.400
α/β/γ90.00090.00090.000
start NX/NY/NZ494949
NX/NY/NZ969696
MAP C/R/S123
start NC/NR/NS-96-96-96
NC/NR/NS192192192
D min/max/mean-4.13410.415-0.000

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Supplemental data

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Sample components

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Entire : Sec13/31 bound to Sec23/24

EntireName: Sec13/31 bound to Sec23/24
Components
  • Sample: Sec13/31 bound to Sec23/24
  • Organelle or cellular component: COPII coat

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Supramolecule #1000: Sec13/31 bound to Sec23/24

SupramoleculeName: Sec13/31 bound to Sec23/24 / type: sample / ID: 1000
Oligomeric state: 60 Sec13-31 heterotetramers bound to 120 Sec23-24 heterodimers
Number unique components: 4
Molecular weightTheoretical: 44.8 MDa

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Supramolecule #1: COPII coat

SupramoleculeName: COPII coat / type: organelle_or_cellular_component / ID: 1 / Name.synonym: Sec13-31 and Sec23-24 / Recombinant expression: Yes
Ref GO0: GO:0006888
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Location in cell: cytosol
Molecular weightExperimental: 44.8 MDa / Theoretical: 44.8 MDa
Recombinant expressionOrganism: Insect cells / Recombinant plasmid: bacmid

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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

BufferpH: 6.8
Details: 50 mM MES pH 6.8, 700 mM KOAc, 1 mM MgOAc, 1 mM DTT
GridDetails: 400 mesh grid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 98 K / Instrument: OTHER / Details: Vitrification instrument: vitrobot / Method: blot for 3 seconds before plunging

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureAverage: 88 K
Alignment procedureLegacy - Astigmatism: astigmatism corrected automatically with Leginon.
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 20 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 29000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus min: 10.0 µm / Nominal magnification: 29000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

DetailsData was automatically collected using Leginon. Data was processed automatically with Appion. Particles were picked manually.
CTF correctionDetails: each particle
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 43.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Details: Final map was lowpass filtered to 43 angstroms / Number images used: 12120
Final two d classificationNumber classes: 212

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Atomic model buiding 1

Initial modelPDB ID:

2pm9

SoftwareName: Normal mode-based flexible fitting (nmff) and chimera
DetailsProtocol: normal modes flexible fitting and rigid body. A bend was modeled into Sec13-31 using the program nmff. Sec13-31 and Sec23-24 were separately fitted into the cryoEM density using the program Chimera.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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Atomic model buiding 2

Initial modelPDB ID:

2pm6

SoftwareName: nmff and chimera
DetailsProtocol: normal modes flexible fitting and rigid body. A bend was modeled into Sec13-31 using the program nmff. Sec13-31 and Sec23-24 were separately fitted into the cryoEM density using the program Chimera.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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Atomic model buiding 3

Initial modelPDB ID:

1m2v

SoftwareName: nmff and chimera
DetailsProtocol: normal modes flexible fitting and rigid body. A bend was modeled into Sec13-31 using the program nmff. Sec13-31 and Sec23-24 were separately fitted into the cryoEM density using the program Chimera.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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