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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 GOdivclassse qspanoncli ckpopupspa nclassgree n(this)spandata popltspanc lassquotlo adingbarqu otgtltimgs rcquotimgl oadinggifq uotdecodin gquotasync quotgtltsp angtdataur lajaxphp?m odetaxoamp ...
divclassse qspanoncli ckpopupspa nclassgree n(this)spandata popltspanc lassquotlo adingbarqu otgtltimgs rcquotimgl oadinggifq uotdecodin gquotasync quotgtltsp angtdataur lajaxphp?m odetaxoamp kGO3A00068 88ampajax1 classpoptr giGO000688 8ispandiv
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
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 29000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / 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
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
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: each particle
Final two d classificationNumber classes: 212
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
DetailsData was automatically collected using Leginon. Data was processed automatically with Appion. Particles were picked manually.

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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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