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- EMDB-0149: PTC3 holotoxin complex from Photorhabdus luminecens in prepore st... -

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Basic information

Entry
Database: EMDB / ID: 0149
TitlePTC3 holotoxin complex from Photorhabdus luminecens in prepore state (TcdA1, TcdB2, TccC3)
Map dataPhotorhabdus luminescens ABC holotoxin Volume is filtered according to its local resolution
SamplePTC3 holotoxin complex in prepore state (5 x TcdA1, 1 x TcdB2, 1 x TccC3):
(TcdA1) x 2 / TcdB2/TccC3 / TcdB2,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 / 3.95 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: 6h6e

SummaryFull reportAbout validation report
DateDeposition: Jul 27, 2018 / Header (metadata) release: Sep 5, 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: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Map surface with fitted models
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_0149.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
1.14 Å/pix.
= 547.2 Å
480 pix
1.14 Å/pix.
= 547.2 Å
480 pix
1.14 Å/pix.
= 547.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.14 Å
Density
Contour Level:0.02 (by author), 0.02 (movie #1):
Minimum - Maximum-0.13690102 - 0.12409625
Average (Standard dev.)0.00017070811 (0.0030184903)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions480480480
Origin0.00.00.0
Limit479.0479.0479.0
Spacing480480480
CellA=B=C: 547.2 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.141.141.14
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z547.200547.200547.200
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-0.1370.1240.000

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Supplemental data

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Sample components

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Entire PTC3 holotoxin complex in prepore state (5 x TcdA1, 1 x TcdB2, 1 ...

EntireName: PTC3 holotoxin complex in prepore state (5 x TcdA1, 1 x TcdB2, 1 x TccC3)
Number of components: 5

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Component #1: protein, PTC3 holotoxin complex in prepore state (5 x TcdA1, 1 x ...

ProteinName: PTC3 holotoxin complex in prepore state (5 x TcdA1, 1 x TcdB2, 1 x TccC3)
Recombinant expression: No
SourceSpecies: Photorhabdus luminescens (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, TcdA1

ProteinName: TcdA1 / Details: 5 TcdA1 subunits in the 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

ProteinName: TcdB2/TccC3 / Details: 1 TcdB2/TccC3 monomer in the holotoxin complex / 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

ProteinName: TcdB2,TccC3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 273.678656 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 / Humidity: 94 % / Details: blot 3 sec before plunging.

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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
LensImaging 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: 3068

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 89148
3D reconstructionSoftware: SPHIRE / Resolution: 3.95 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Target criteria: Model to Map FSC / Refinement space: REAL
Input PDB model: 1VW1, 4O9X, 1VW1, 1VW1, 1VW1, 1VW1
Chain ID: A, A, B, C, D, E

Overall bvalue: 68.030000000000001
Output model

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