[English] 日本語
Yorodumi
- EMDB-1511: COPII coat -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: EMD-1511
TitleCOPII coat
Map data
SampleSec13/31 bound to Sec23/24:
COPII coat
Keywordsvesicle trafficking / COPII / icosidodecahedron / secretory pathway / endoplasmic reticulum / automation
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 43 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.
DateDeposition: May 24, 2008 / Header (metadata) release: May 27, 2008 / Map release: Mar 31, 2009 / Update: Mar 31, 2009

-
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
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_1511.map.gz / Format: CCP4 / Size: 26.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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
Contour LevelPrimary: 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

-
Supplemental data

-
Sample components

-
Entire Sec13/31 bound to Sec23/24

EntireName: Sec13/31 bound to Sec23/24 / Number of components: 4
Oligomeric State: 60 Sec13-31 heterotetramers bound to 120 Sec23-24 heterodimers
MassTheoretical: 44.8 MDa

-
Component #1: cellular-component, COPII coat

Cellular-componentName: COPII coat / a.k.a: Sec13-31 and Sec23-24 / Recombinant expression: Yes
MassTheoretical: 44.8 MDa / Experimental: 44.8 MDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Insect cells / Vector: bacmid
Source (natural)Location in cell: cytosol
External referencesGene Ontology: endoplasmic reticulum to Golgi vesicle-mediated transport

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionBuffer solution: 50 mM MES pH 6.8, 700 mM KOAc, 1 mM MgOAc, 1 mM DTT
pH: 6.8
Support film400 mesh grid
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 98 K / Humidity: 100 % / Method: blot for 3 seconds before plunging / Details: Vitrification instrument: vitrobot

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 29000 X (nominal), 29000 X (calibrated)
Astigmatism: astigmatism corrected automatically with Leginon.
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 10000 - nm
Specimen HolderHolder: Side entry liquid nitrogen-cooled cryo specimen holder
Model: GATAN LIQUID NITROGEN / Temperature: 88
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of class averages: 212 / Number of projections: 12120
Details: Data was automatically collected using Leginon. Data was processed automatically with Appion. Particles were picked manually.
Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: projection matching / Software: EMAN / CTF correction: each particle / Details: Final map was lowpass filtered to 43 angstroms / Resolution: 43 Å / Resolution method: FSC 0.5

-
Atomic model buiding

Modeling #1Software: Normal mode-based flexible fitting (nmff), chimera
Refinement protocol: flexible / Refinement space: REAL
Details: Protocol: 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.
Input PDB model: 2pm9
Modeling #2Software: nmff, chimera / Refinement protocol: flexible / Refinement space: REAL
Details: Protocol: 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.
Input PDB model: 2pm6
Modeling #3Software: nmff, chimera / Refinement protocol: flexible / Refinement space: REAL
Details: Protocol: 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.
Input PDB model: 1m2v

+
About Yorodumi

-
News

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at PDBe / Contact to PDBj

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more