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- EMDB-0150: PTC3 holotoxin complex from Photorhabdus luminiscens - Mutant TcC... -

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Basic information

Entry
Database: EMDB / ID: 0150
TitlePTC3 holotoxin complex from Photorhabdus luminiscens - Mutant TcC-D651A
Map dataCryoEM structure of the Photorhadbus luminescens ABC-D651A holotoxin complex
SamplePTC3 holotoxin complex in prepore state - Mutant TcC-D651A:
(TcdA1) x 2 / TcdB2/TccC3-D651A / TcdB2,TccC3,TccC3
Function / homologySalmonella virulence plasmid 65kDa B protein / Insecticidal toxin complex/plasmid virulence protein / Insecticide toxin TcdB middle/C-terminal / Insecticide toxin TcdB middle/N-terminal / Rhs repeat-associated core / Salmonella virulence plasmid 65kDa B protein / Salmonella virulence plasmid 28.1kDa A protein / Insecticide toxin TcdB middle/C-terminal region / Insecticide toxin TcdB middle/N-terminal region / self proteolysis ...Salmonella virulence plasmid 65kDa B protein / Insecticidal toxin complex/plasmid virulence protein / Insecticide toxin TcdB middle/C-terminal / Insecticide toxin TcdB middle/N-terminal / Rhs repeat-associated core / Salmonella virulence plasmid 65kDa B protein / Salmonella virulence plasmid 28.1kDa A protein / Insecticide toxin TcdB middle/C-terminal region / Insecticide toxin TcdB middle/N-terminal region / self proteolysis / identical protein binding / cytoplasm / TccC3 / TcdB2 / TcdA1
Function and homology information
SourcePhotorhabdus luminescens (bacteria)
Methodsingle particle reconstruction / cryo EM / 3.72 Å resolution
AuthorsGatsogiannis C / Merino F / Roderer D / Balchin D / Schubert E / Kuhlee A / Hayer-Hartl M / Raunser S
CitationJournal: Nature / Year: 2018
Title: Tc toxin activation requires unfolding and refolding of a β-propeller.
Authors: Christos Gatsogiannis / Felipe Merino / Daniel Roderer / David Balchin / Evelyn Schubert / Anne Kuhlee / Manajit Hayer-Hartl / Stefan Raunser
Validation ReportPDB-ID: 6h6f

SummaryFull reportAbout validation report
DateDeposition: Jul 27, 2018 / Header (metadata) release: Aug 15, 2018 / Map release: Oct 3, 2018 / Last update: Nov 14, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Map surface with fitted models
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_0150.map.gz (map file in CCP4 format, 442369 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
480 pix
1.1 Å/pix.
= 528. Å
480 pix
1.1 Å/pix.
= 528. Å
480 pix
1.1 Å/pix.
= 528. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density
Contour Level:0.03 (by author), 0.03 (movie #1):
Minimum - Maximum-0.11320373 - 0.14066413
Average (Standard dev.)0.0002554831 (0.0031504855)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions480480480
Origin0.00.00.0
Limit479.0479.0479.0
Spacing480480480
CellA=B=C: 528.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z528.000528.000528.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.1130.1410.000

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Supplemental data

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Sample components

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Entire PTC3 holotoxin complex in prepore state - Mutant TcC-D651A

EntireName: PTC3 holotoxin complex in prepore state - Mutant TcC-D651A
Details: The catalytic protease spartyl protease site is deleted
Number of components: 5

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Component #1: protein, PTC3 holotoxin complex in prepore state - Mutant TcC-D651A

ProteinName: PTC3 holotoxin complex in prepore state - Mutant TcC-D651A
Details: The catalytic protease spartyl protease site is deleted
Recombinant expression: No
MassTheoretical: 1.7 MDa

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Component #2: protein, TcdA1

ProteinName: TcdA1 / Details: 5 TcdA1 protomers in the PTC3 holotoxin complex / Recombinant expression: No
SourceSpecies: Photorhabdus luminescens (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, TcdB2/TccC3-D651A

ProteinName: TcdB2/TccC3-D651A
Details: 1 TcdB2/TccC3-D651A monomer in the PTC3 holotoxin complex. The catalytic aspartyl protease site of TccC3 is deleted.
Recombinant expression: No
SourceSpecies: Photorhabdus luminescens (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: protein, TcdA1

ProteinName: TcdA1 / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 283.229406 kDa
SourceSpecies: Photorhabdus luminescens (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #5: protein, TcdB2,TccC3,TccC3

ProteinName: TcdB2,TccC3,TccC3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 273.634656 kDa
SourceSpecies: Photorhabdus luminescens (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 8
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen 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: 2.2 e/Å2 / Illumination mode: OTHER
LensMagnification: 59000.0 X (nominal) / Cs: 0 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 4958

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 132000
3D reconstructionSoftware: SPHIRE / Resolution: 3.72 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Target criteria: Model to Map FSC / Refinement space: REAL / Overall bvalue: 49.43
Output model

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