|Entry||Database: PDB / ID: 5myu|
|Title||VipA-N2/VipB contracted sheath of type VI secretion system|
|Keywords||PROTEIN TRANSPORT / Bacterial type VI secretion system / protein export / protein transport|
|Specimen source||Vibrio cholerae / bacteria / コレラ菌, ビブリオ・コレラエ|
|Method||Electron microscopy (4 Å resolution / Helical array / Helical)|
|Authors||Wang, J. / Brackmann, B. / Castano-Diez, D. / Kudryashev, M. / Goldie, D. / Maier, T. / Stahlberg, H. / Basler, M.|
|Citation||Nat Microbiol, 2017, 2, 1507-1512|
SummaryFull reportAbout validation report
|Date||Deposition: Jan 27, 2017 / Release: Aug 2, 2017|
Downloads & links
a: Uncharacterized protein
A: Type VI secretion system protein ImpC
b: Uncharacterized protein
B: Type VI secretion system protein ImpC
c: Uncharacterized protein
C: Type VI secretion system protein ImpC
d: Uncharacterized protein
D: Type VI secretion system protein ImpC
e: Uncharacterized protein
E: Type VI secretion system protein ImpC
f: Uncharacterized protein
F: Type VI secretion system protein ImpC
Mass: 13916.752 Da / Num. of mol.: 6
Source: (gene. exp.) Vibrio cholerae / bacteria / コレラ菌, ビブリオ・コレラエ
References: UniProt: A0A023PRF3
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: HELICAL ARRAY / Reconstruction method: HELICAL|
|Component||Name: Type IV secretion system sheath-tube / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: 1, 2 / Source: NATURAL|
|Source (natural)||Organism: Vibrio cholerae|
|Buffer solution||pH: 7.5|
|Specimen||Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Microscope model: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELD|
|Image recording||Electron dose: 30 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Helical symmerty||Angular rotation/subunit: 29.4 deg. / Axial rise/subunit: 21.7 Å / Axial symmetry: C6|
|3D reconstruction||Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 7000 / Number of class averages: 1 / Symmetry type: HELICAL|
|Atomic model building||Ref protocol: RIGID BODY FIT|
-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.
+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)
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