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- EMDB-71671: Thin Flagellar Filament from T. denticola -

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Basic information

Entry
Database: EMDB / ID: EMD-71671
TitleThin Flagellar Filament from T. denticola
Map data
Sample
  • Complex: FlaB3 molecules from the lattice of a thin periplasmic flagellar filament purified from planktonic T. denticola
    • Protein or peptide: Flagellin
  • Ligand: (2S,4S,5S,6S)-5-carbamoyl-4-hydroxy-6-{(1S)-1-hydroxy-1-[(2R,4S,5R)-4,5,6-trihydroxy-2-methoxyhexanamido]ethyl}-2-methoxyoxane-2-carboxylic acid
Keywordsflagella / periplasmic flagella / bacterial flagella / filament / PROTEIN FIBRIL
Function / homologyperiplasmic flagellum / Flagellin, C-terminal domain, subdomain 2 / Flagellin, C-terminal domain / Bacterial flagellin C-terminal helical region / Flagellin / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region / structural molecule activity / Flagellin
Function and homology information
Biological speciesTreponema denticola ATCC 35405 (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsTroman LA / Paul B / Ghosal D
Funding support Australia, 2 items
OrganizationGrant numberCountry
Other privateCGCPT00060 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1196924 Australia
CitationJournal: To Be Published
Title: Thin Flagellar Filament from T. denticola
Authors: Troman LA / Paul B / Ghosal D
History
DepositionJul 10, 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_71671.png

Downloads & links

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Map

FileDownload / File: emd_71671.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 448 pix.
= 373.184 Å		0.83 Å/pix.
x 448 pix.
= 373.184 Å		0.83 Å/pix.
x 448 pix.
= 373.184 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.833 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.003
Minimum - Maximum-0.0052369577 - 0.011890285
Average (Standard dev.)0.000017305136 (±0.0006975056)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 373.184 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_71671_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: deepEMhancer sharpened map

Fileemd_71671_additional_1.map
AnnotationdeepEMhancer sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half map 2

Fileemd_71671_half_map_1.map
AnnotationUnfiltered half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half map 1

Fileemd_71671_half_map_2.map
AnnotationUnfiltered half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : FlaB3 molecules from the lattice of a thin periplasmic flagellar ...

EntireName: FlaB3 molecules from the lattice of a thin periplasmic flagellar filament purified from planktonic T. denticola
Components
  • Complex: FlaB3 molecules from the lattice of a thin periplasmic flagellar filament purified from planktonic T. denticola
    • Protein or peptide: Flagellin
  • Ligand: (2S,4S,5S,6S)-5-carbamoyl-4-hydroxy-6-{(1S)-1-hydroxy-1-[(2R,4S,5R)-4,5,6-trihydroxy-2-methoxyhexanamido]ethyl}-2-methoxyoxane-2-carboxylic acid

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Supramolecule #1: FlaB3 molecules from the lattice of a thin periplasmic flagellar ...

SupramoleculeName: FlaB3 molecules from the lattice of a thin periplasmic flagellar filament purified from planktonic T. denticola
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Treponema denticola ATCC 35405 (bacteria)

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Macromolecule #1: Flagellin

MacromoleculeName: Flagellin / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Treponema denticola ATCC 35405 (bacteria) / Strain: ATCC 35405
Molecular weightTheoretical: 30.973941 KDa
SequenceString: MIINHNMSAM FAQRQGGVNE LHLAKNIEKL SSAQRINRAG DDASGLAVSE KMRSQIRGLN QAGQNIQNGV SFIQATEGYL GETTDIIQR LRELAIQASN GIYSAEDRMQ IQVEVSQLVD EVDRIASHAQ FNGMNILTGR FAQDSVTGPM QLHVGANMDQ R EKIYIGTM ...String:
MIINHNMSAM FAQRQGGVNE LHLAKNIEKL SSAQRINRAG DDASGLAVSE KMRSQIRGLN QAGQNIQNGV SFIQATEGYL GETTDIIQR LRELAIQASN GIYSAEDRMQ IQVEVSQLVD EVDRIASHAQ FNGMNILTGR FAQDSVTGPM QLHVGANMDQ R EKIYIGTM TATALGIIGA QQGGEDKMIS MSSVDGANMA LGALDNALKQ INKQRADLGA YQNRFEMAYD GIAIAAENMQ AA ESRIRDA DMAKEIVDYT KNQILIQSGT AMLAQANAQP QAVVRLLQ

UniProtKB: Flagellin

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Macromolecule #2: (2S,4S,5S,6S)-5-carbamoyl-4-hydroxy-6-{(1S)-1-hydroxy-1-[(2R,4S,5...

MacromoleculeName: (2S,4S,5S,6S)-5-carbamoyl-4-hydroxy-6-{(1S)-1-hydroxy-1-[(2R,4S,5R)-4,5,6-trihydroxy-2-methoxyhexanamido]ethyl}-2-methoxyoxane-2-carboxylic acid
type: ligand / ID: 2 / Number of copies: 36 / Formula: A1CIM
Molecular weightTheoretical: 454.426 Da

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: LEICA EM GP / Details: The sample was back blotted.
DetailsPeriplasmic flagella purified from planktonic T. denticola

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 7082 / Average exposure time: 2.67 sec. / Average electron dose: 57.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
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

Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 179219
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: NONE
Segment selectionNumber selected: 665964 / Software - Name: crYOLO (ver. 1.9.9) / Details: Particle picking using crYOLO filament picker.
Startup modelType of model: EMDB MAP
EMDB ID:

12345


Details: Tomographic reconstructions for the thick and thin filaments were used as the initial models for 3D classification. These will be submitted to EMDB as part of the same publication.
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: experimental model
Details: ModelAngelo generated the initial model from the cryo-EM data.
DetailsModelAngelo automated the model builder was used to generate the initial model for refinement. This first given the full proteome for T.denticola and subsequently only the fasta file for FlaB3.
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-9pil:
Thin Flagellar Filament from T. denticola

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