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- EMDB-71716: Sub-tomogram average of thick flagellar filament of T. denticola -

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Basic information

Entry
Database: EMDB / ID: EMD-71716
TitleSub-tomogram average of thick flagellar filament of T. denticola
Map data
Sample
  • Complex: Thick flagellar filaments from T. denticola mono-species biofilm
Keywordsflagella / periplasmic flagella / bacterial flagella / filament / PROTEIN FIBRIL / spirochete flagella
Biological speciesTreponema denticola ATCC 35405 (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 8.9 Å
AuthorsPaul B / Troman LA / Ghosal D
Funding support Australia, 2 items
OrganizationGrant numberCountry
Cumming Global Centre for Pandemic Therapeutics, Peter Doherty Institute for Infection and ImmunityCGCPT00060 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1196924 Australia
CitationJournal: To Be Published
Title: Sub-tomogram average of thick flagellar filament of T. denticola
Authors: Paul B / Troman LA / Ghosal D
History
DepositionJul 15, 2025-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71716.png

Downloads & links

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Map

FileDownload / File: emd_71716.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.6 Å/pix.
x 220 pix.
= 352.66 Å		1.6 Å/pix.
x 220 pix.
= 352.66 Å		1.6 Å/pix.
x 220 pix.
= 352.66 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.603 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.34237555 - 0.8225906
Average (Standard dev.)0.025053134 (±0.06940497)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 352.66 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_71716_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_71716_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_71716_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Thick flagellar filaments from T. denticola mono-species biofilm

EntireName: Thick flagellar filaments from T. denticola mono-species biofilm
Components
  • Complex: Thick flagellar filaments from T. denticola mono-species biofilm

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Supramolecule #1: Thick flagellar filaments from T. denticola mono-species biofilm

SupramoleculeName: Thick flagellar filaments from T. denticola mono-species biofilm
type: complex / ID: 1 / Parent: 0
Details: Thick flagellar filaments were averaged from the tomograms obtained from T. denticola mono-species biofilm.
Source (natural)Organism: Treponema denticola ATCC 35405 (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Average exposure time: 0.8 sec. / Average electron dose: 2.92 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated magnification: 52000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 4.0 µm / Nominal magnification: 52000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsImages motion corrected using MotionCorr3. Tilt series manually aligned and reconstructed using IMOD.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number subtomograms used: 2192
ExtractionNumber tomograms: 65 / Number images used: 4848 / Software - Name: RELION (ver. 4)
CTF correctionSoftware - Name: IMOD (ver. 4.11.25) / Type: PHASE FLIPPING ONLY
Final 3D classificationSoftware - Name: RELION (ver. 4)
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 4)
FSC plot (resolution estimation)

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