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- EMDB-8399: Single particle cryo-EM reconstruction of the Salmonella SPI-1 ty... -

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Basic information

Entry
Database: EMDB / ID: 8399
TitleSingle particle cryo-EM reconstruction of the Salmonella SPI-1 type III secretion injectisome secretin InvG at 3.6 Angstrom resolution
SampleType III injectisome basal body
SourceSalmonella enterica subsp. enterica serovar typhimurium / bacteria
Map data15x symmetry averaged single particle cryo-EM reconstruction of the Salmonella type III secretion system secretin InvG at 3.6 Angstrom resolution
Methodsingle particle reconstruction, at 3.6 Å resolution
AuthorsWorrall LJ / Hong C
CitationNature, 2016

Nature, 2016 Yorodumi Papers
Near-atomic-resolution cryo-EM analysis of the Salmonella T3S injectisome basal body.
L J Worrall / C Hong / M Vuckovic / W Deng / J R C Bergeron / D D Majewski / R K Huang / T Spreter / B B Finlay / Z Yu / N C J Strynadka

Validation ReportPDB-ID: 5tcq

SummaryFull reportAbout validation report
DateDeposition: Sep 15, 2016 / Header (metadata) release: Nov 9, 2016 / Map release: Dec 21, 2016 / Last update: Sep 13, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.08
  • Imaged by UCSF CHIMERA
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  • Surface view colored by cylindrical radius
  • Surface level: 0.08
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5tcq
  • Surface level: 0.08
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5tcq
  • Surface level: 0.08
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

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Map

Fileemd_8399.map.gz (map file in CCP4 format, 108001 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
300 pix
1.71 Å/pix.
= 513. Å
300 pix
1.71 Å/pix.
= 513. Å
300 pix
1.71 Å/pix.
= 513. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.71 Å
Density
Contour Level:0.08 (by author), 0.08 (movie #1):
Minimum - Maximum-0.18196891 - 0.3536772
Average (Standard dev.)0.0008786313 (0.0072768456)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions300300300
Origin000
Limit299299299
Spacing300300300
CellA=B=C: 513 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.711.711.71
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z513.000513.000513.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.1820.3540.001

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Supplemental data

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Sample components

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Entire Type III injectisome basal body

EntireName: Type III injectisome basal body / Details: PrgH130-392 mutant / Number of components: 2
MassTheoretical: 2 MDa

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Component #1: protein, Type III injectisome basal body

ProteinName: Type III injectisome basal body / Details: PrgH130-392 mutant / Recombinant expression: No
MassTheoretical: 2 MDa
SourceSpecies: Salmonella enterica subsp. enterica serovar typhimurium / bacteria

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Component #2: protein, Protein InvG

ProteinName: Protein InvG / Recombinant expression: No
MassTheoretical: 61.835559 kDa
SourceSpecies: Salmonella enterica subsp. enterica serovar typhimurium / bacteria

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 10 mg/ml / pH: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 90 %

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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: 1.3 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 64000 X (nominal), 29240 X (calibrated) / Cs: 0.01 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 3000 nm / Energy filter: Gatan GIF / Energy window: 0-20 eV
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: K ( 80 - 80 K)
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2685 / Sampling size: 5 microns

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C15 (15 fold cyclic) / Number of projections: 83900
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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  • 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

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