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- EMDB-3567: VipA-N2/VipB contracted sheath of type VI secretion system -

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Basic information

Entry
Database: EMDB / ID: 3567
TitleVipA-N2/VipB contracted sheath of type VI secretion system
SampleType VI secretion system sheath
SourceVibrio cholerae / bacteria / コレラ菌, ビブリオ・コレラエ
Map data
Methodhelical reconstruction, at 4 Å resolution
AuthorsWang J / Brackmann M / Castano-Diez D / Kudryashev M / Goldie K / Maier T / Stahlberg H / Basler M
CitationNat Microbiol, 2017

Nat Microbiol, 2017 Yorodumi Papers
Cryo-EM structure of the extended type VI secretion system sheath-tube complex.
Jing Wang / Maximilian Brackmann / Daniel Castaño-Díez / Mikhail Kudryashev / Kenneth N Goldie / Timm Maier / Henning Stahlberg / Marek Basler

Validation ReportPDB-ID: 5myu

SummaryFull reportAbout validation report
DateDeposition: Jan 10, 2017 / Header (metadata) release: Feb 8, 2017 / Map release: Aug 2, 2017 / Last update: Oct 11, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5myu
  • Surface level: 0.02
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5myu
  • Surface level: 0.02
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_3567.map.gz (map file in CCP4 format, 66356 KB)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
128 pix
1.04 Å/pix.
= 132.992 Å
360 pix
1.04 Å/pix.
= 374.04 Å
360 pix
1.04 Å/pix.
= 374.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.039 Å
Density
Contour Level:0.02 (by author), 0.02 (movie #1):
Minimum - Maximum-0.05793927 - 0.097034894
Average (Standard dev.)0.0009659687 (0.010127282)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions360360128
Origin7676192
Limit435435319
Spacing360360128
CellA: 374.04 Å / B: 374.04 Å / C: 132.992 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0391.0391.039
M x/y/z360360128
origin x/y/z0.0000.0000.000
length x/y/z374.040374.040132.992
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS7676192
NC/NR/NS360360128
D min/max/mean-0.0580.0970.001

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Supplemental data

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Sample components

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Entire Type VI secretion system sheath

EntireName: Type VI secretion system sheath / Number of components: 3

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Component #1: cellular-component, Type VI secretion system sheath

Cellular-componentName: Type VI secretion system sheath / Recombinant expression: No
SourceSpecies: Vibrio cholerae / bacteria / コレラ菌, ビブリオ・コレラエ

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Component #2: protein, VipA

ProteinName: VipA / Recombinant expression: No

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Component #3: protein, VipB

ProteinName: VipB / Recombinant expression: No

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Experimental details

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Sample preparation

Specimen statehelical array
Helical parametersAxial symmetry: C6 (6 fold cyclic) / Delta z: 21.7 Å / Delta phi: 29.4 deg.
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 30 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 186
Raw dataEMPIAR-10085 (Title: Cryo EM of Type VI Secretion System VipA-N2/VipB contracted sheath
Data size: 74.0
Data #1: Unaligned multi-frame micrographs of T6SS VipA-N2/VipB contracted sheath [micrographs - multiframe])

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionSoftware: RELION / Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Details: RELION2, 3D auto-refine
FSC plot (resolution assessment)

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Atomic model buiding

Output model

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