|Entry||Database: EMDB / ID: 3566|
|Title||VipA-N3, non-contractile sheath of the type VI secretion system|
|Sample||vipA-N3/vipB noncontractile sheath with Hcp tube|
|Source||Vibrio cholerae / bacteria / コレラ菌, ビブリオ・コレラエ|
|Map data||Postprocessed in Relion2, average resolution is 3.7A.|
|Method||helical reconstruction, at 3.7 Å resolution|
|Authors||Wang J / Brackmann M / Castano-Diez D / Kudryashev M / Goldie G / Maier T / Stahlberg H / Basler M|
|Citation||Nat Microbiol, 2017, 2, 1507-1512|
|Validation Report||PDB-ID: 5mxn|
About validation report
|Date||Deposition: Jan 9, 2017 / Header (metadata) release: Feb 8, 2017 / Map release: Aug 2, 2017 / Last update: Nov 8, 2017|
Downloads & links
|File||emd_3566.map.gz (map file in CCP4 format, 67109 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 1.039 Å|
CCP4 map header:
-Entire vipA-N3/vipB noncontractile sheath with Hcp tube
|Entire||Name: vipA-N3/vipB noncontractile sheath with Hcp tube / Number of components: 4|
-Component #1: cellular-component, vipA-N3/vipB noncontractile sheath with Hcp tube
|Cellular-component||Name: vipA-N3/vipB noncontractile sheath with Hcp tube / Recombinant expression: No|
|Source||Species: Vibrio cholerae / bacteria / コレラ菌, ビブリオ・コレラエ|
-Component #2: protein, Hcp
|Protein||Name: Hcp / Recombinant expression: No|
-Component #3: protein, VipA
|Protein||Name: VipA / Recombinant expression: No|
-Component #4: protein, vipB
|Protein||Name: vipB / Recombinant expression: No|
|Specimen state||helical array|
|Helical parameters||Axial symmetry: C6 (6 fold cyclic) / Delta z: 37.8 Å / Delta phi: 23.5 deg.|
|Sample solution||pH: 7.5|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 30 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: GATAN K2 (4k x 4k)|
|Raw data||EMPIAR-10086 (Title: Cryo EM of Type VI Secretion System VipA-N3/VipB/Hcp complex|
Data size: 26.2
Data #1: Unaligned multi-frame micrographs of T6SS VipA-N3/VipB/Hcp complex [micrographs - multiframe])
|Processing||Method: helical reconstruction|
|3D reconstruction||Software: RELION / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF|
-Atomic model buiding
-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.
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External links: The 2017 Nobel Prize in Chemistry - Press Release
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