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- EMDB-1759: Double helical filaments of an N-terminal thioredoxin fusion of TubZ -

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Basic information

Entry
Database: EMDB / ID: EMD-1759
TitleDouble helical filaments of an N-terminal thioredoxin fusion of TubZ
Map dataDouble helical filaments of a Thioredoxin N-terminal fusion of TubZ (Q8KNP3_BACTI) from bacillus thuringiensis serovar israelensis (ATCC 35646). density for the thioredoxin fusion of TubZ to remove positive density on the outer boundary of the negative stain and unconnected to the main helix.
Sample
  • Sample: Double helical filament of Trx-TubZ
  • Protein or peptide: Cytomotive filament
KeywordsCytoskeleton / DNA segregation / FtsZ / FtsZ-like / pBtoxis / pbt156 / plasmid partitioning / RepX / tubulin / tubulin-like / TubZ
Biological speciesBacillus thuringiensis (bacteria)
Methodhelical reconstruction / negative staining / Resolution: 35.0 Å
AuthorsAylett CHS / Amos LA / Lowe J
CitationJournal: Proc Natl Acad Sci U S A / Year: 2010
Title: Filament structure of bacterial tubulin homologue TubZ.
Authors: Christopher H S Aylett / Qing Wang / Katharine A Michie / Linda A Amos / Jan Löwe /
Abstract: Low copy number plasmids often depend on accurate partitioning systems for their continued survival. Generally, such systems consist of a centromere-like region of DNA, a DNA-binding adaptor, and a ...Low copy number plasmids often depend on accurate partitioning systems for their continued survival. Generally, such systems consist of a centromere-like region of DNA, a DNA-binding adaptor, and a polymerizing cytomotive filament. Together these components drive newly replicated plasmids to opposite ends of the dividing cell. The Bacillus thuringiensis plasmid pBToxis relies on a filament of the tubulin/FtsZ-like protein TubZ for its segregation. By combining crystallography and electron microscopy, we have determined the structure of this filament. We explain how GTP hydrolysis weakens the subunit-subunit contact and also shed light on the partitioning of the plasmid-adaptor complex. The double helical superstructure of TubZ filaments is unusual for tubulin-like proteins. Filaments of ParM, the actin-like partitioning protein, are also double helical. We suggest that convergent evolution shapes these different types of cytomotive filaments toward a general mechanism for plasmid separation.
History
DepositionJul 9, 2010-
Header (metadata) releaseJul 23, 2010-
Map releaseOct 29, 2010-
UpdateApr 20, 2016-
Current statusApr 20, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 300
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 300
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1759.png

Downloads & links

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Map

FileDownload / File: emd_1759.map.gz / Format: CCP4 / Size: 666 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDouble helical filaments of a Thioredoxin N-terminal fusion of TubZ (Q8KNP3_BACTI) from bacillus thuringiensis serovar israelensis (ATCC 35646). density for the thioredoxin fusion of TubZ to remove positive density on the outer boundary of the negative stain and unconnected to the main helix.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
4 Å/pix.
x 86 pix.
= 344. Å		4.4 Å/pix.
x 45 pix.
= 198. Å		4.4 Å/pix.
x 45 pix.
= 198. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX: 4.4 Å / Y: 4.4 Å / Z: 4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 200.0 / Movie #1: 300
Minimum - Maximum-1438.509999999999991 - 1784.529999999999973
Average (Standard dev.)-728.807000000000016 (±799.323999999999955)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin000
Dimensions454586
Spacing454586
CellA: 198 Å / B: 198 Å / C: 344 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.44.44
M x/y/z454586
origin x/y/z0.0000.0000.000
length x/y/z198.000198.000344.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ454586
MAP C/R/S213
start NC/NR/NS000
NC/NR/NS454586
D min/max/mean-1438.5131784.530-728.807

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Supplemental data

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Sample components

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Entire : Double helical filament of Trx-TubZ

EntireName: Double helical filament of Trx-TubZ
Components
  • Sample: Double helical filament of Trx-TubZ
  • Protein or peptide: Cytomotive filament

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Supramolecule #1000: Double helical filament of Trx-TubZ

SupramoleculeName: Double helical filament of Trx-TubZ / type: sample / ID: 1000 / Details: Negatively stained / Oligomeric state: Dimer / Number unique components: 1

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Macromolecule #1: Cytomotive filament

MacromoleculeName: Cytomotive filament / type: protein_or_peptide / ID: 1 / Name.synonym: Cytomotive filament / Oligomeric state: Double filament / Recombinant expression: Yes
Source (natural)Organism: Bacillus thuringiensis (bacteria) / Strain: Serovar israelensis / Location in cell: Cytoplasm
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pET28a

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Experimental details

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Structure determination

Methodnegative staining
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.5
Details: 50 mM NaHEPES pH7.5, 150 mM KCl, 5 mM MgCl2 1 mM GTPyS
StainingType: NEGATIVE / Details: 1% Uranyl Acetate
GridDetails: CuRh 300 mesh
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI 12
Image recordingCategory: CCD / Film or detector model: KODAK SO-163 FILM / Bits/pixel: 8
Electron beamAcceleration voltage: 120 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 67000
Sample stageSpecimen holder: Eucentric / Specimen holder model: SIDE ENTRY, EUCENTRIC

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 35.0 Å / Resolution method: OTHER / Software - Name: MRC / Details: Highest resolution map of three

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