[English] 日本語
- EMDB-5741: Single-particle Electron Microscopy Structure of the TRAPPIII Complex -

Open data

ID or keywords:


no data

Basic information

Database: EMDB / ID: 5741
TitleSingle-particle Electron Microscopy Structure of the TRAPPIII Complex
SampleRecombinant TRAPPIII complex
SourceSaccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Map dataReconstruction of yeast TRAPPIII complex, filtered to 22 Angstrom resolution
Methodsingle particle reconstruction, at 22 Å resolution
AuthorsTan D / Cai Y / Wang J / Zhang J / Menon S / Chou H-T / Ferro-Novick S / Reinisch KM / Walz T
CitationProc. Natl. Acad. Sci. U.S.A., 2013, 110, 19432-19437

Proc. Natl. Acad. Sci. U.S.A., 2013, 110, 19432-19437 Yorodumi Papers
The EM structure of the TRAPPIII complex leads to the identification of a requirement for COPII vesicles on the macroautophagy pathway.
Dongyan Tan / Yiying Cai / Juan Wang / Jinzhong Zhang / Shekar Menon / Hui-Ting Chou / Susan Ferro-Novick / Karin M Reinisch / Thomas Walz

DateDeposition: Aug 12, 2013 / Header (metadata) release: Sep 4, 2013 / Map release: Nov 13, 2013 / Last update: Dec 11, 2013

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.507
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.507
  • Imaged by UCSF CHIMERA
  • Download
3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


Fileemd_5741.map.gz (map file in CCP4 format, 2001 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
80 pix
4.48 Å/pix.
= 358.4 Å
80 pix
4.48 Å/pix.
= 358.4 Å
80 pix
4.48 Å/pix.
= 358.4 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 4.48 Å
Contour Level:0.507 (by author), 0.507 (movie #1):
Minimum - Maximum-0.61211646 - 2.31793046
Average (Standard dev.)0.00571768 (0.11935551)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 358.4 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.484.484.48
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z358.400358.400358.400
start NX/NY/NZ-132-122-147
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.6122.3180.006

Supplemental data

Sample components

Entire Recombinant TRAPPIII complex

EntireName: Recombinant TRAPPIII complex / Number of components: 1 / Oligomeric State: oligomer
MassTheoretical: 254 kDa / Experimental: 254 kDa

Component #1: protein, transport protein particle III

ProteinName: transport protein particle III / Oligomeric Details: monomer / Recombinant expression: Yes / Number of Copies: 1
MassTheoretical: 254 kDa / Experimental: 254 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Vector: pETDuet / Strain: BL21

Experimental details

Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.4 mg/ml / Buffer solution: 20mM Tris-HCl, 300 mM NaCl, 1mM DTT / pH: 8
Support film200 mesh copper grids with thin carbon support, glow discharged
StainingGrids with adsorbed protein stained with 0.75% uranyl format for 20 seconds
VitrificationInstrument: NONE / Cryogen name: NONE

Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 12 / Date: Dec 20, 2010 / Details: low dose setting
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 10 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 67000 X (nominal), 67000 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 1500 nm
Specimen HolderModel: SIDE ENTRY, EUCENTRIC / Tilt Angle: 0 - 60 deg.

Image acquisition

Image acquisitionNumber of digital images: 133 / Scanner: OTHER / Sampling size: 15 microns

Image processing

ProcessingMethod: single particle reconstruction / Number of class averages: 20 / Applied symmetry: C1 (asymmetric) / Number of projections: 1120
Details: Random Conical Tilt reconstruction using Spider scripts
3D reconstructionAlgorithm: random conical tilt / Software: Spider
Details: Final maps were calculated from a dataset of two class-averages
Resolution: 22 Å / Resolution method: FSC 0.5

Atomic model buiding

Modeling #1Software: Chimera / Refinement protocol: flexible / Refinement space: REAL
Input PDB model: 2J3T

About Yorodumi


Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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 / EM Navigator (legacy version) / Yorodumi (legacy version)

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 / EM Navigator (legacy version) / Yorodumi (legacy version)

Read more


Thousand views of thousand structures

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

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more