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- EMDB-71672: Outer Curvature of Thick Flagellar Filament from T.denticola -

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Basic information

Entry
Database: EMDB / ID: EMD-71672
TitleOuter Curvature of Thick Flagellar Filament from T.denticola
Map data
Sample
  • Complex: FlaA1 region of the outer sheath (located at the outer curvature) of thick flagellar filaments purified from planktonic T. denticola
    • Protein or peptide: Flagellar filament outer layer protein
    • 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 / homology
Function and homology information


periplasmic flagellum / bacterial-type flagellum-dependent cell motility / outer membrane-bounded periplasmic space / structural molecule activity
Similarity search - Function
Flagellar filament outer layer protein FlaA, Spirochaetes / Flagellar filament outer layer protein FlaA / Flagellar filament outer layer protein Flaa / 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
Similarity search - Domain/homology
Flagellar filament outer layer protein / Flagellin
Similarity search - Component
Biological speciesTreponema denticola ATCC 35405 (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 2.7 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: Structural basis of biofilm formation by the oral pathogen Treponema denticola
Authors: Troman LA / Paul B
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_71672.png

Downloads & links

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Map

FileDownload / File: emd_71672.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: 0.004
Minimum - Maximum-0.010680403 - 0.021011338
Average (Standard dev.)0.000042492862 (±0.001017042)
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_71672_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_71672_additional_1.map
Projections & Slices
AxesZYX

Projections

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_71672_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_71672_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 : FlaA1 region of the outer sheath (located at the outer curvature)...

EntireName: FlaA1 region of the outer sheath (located at the outer curvature) of thick flagellar filaments purified from planktonic T. denticola
Components
  • Complex: FlaA1 region of the outer sheath (located at the outer curvature) of thick flagellar filaments purified from planktonic T. denticola
    • Protein or peptide: Flagellar filament outer layer protein
    • 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: FlaA1 region of the outer sheath (located at the outer curvature)...

SupramoleculeName: FlaA1 region of the outer sheath (located at the outer curvature) of thick flagellar filaments purified from planktonic T. denticola
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2, #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)
Molecular weightTheoretical: 31.598715 KDa
SequenceString: MIINHNMSAM FSQRTLGHTH LLNQKNIEKL SSGLRINRAG DDASGLAVSE KMRSQIRGLN QASANAQNGI SFIQVAEAFL QETTDVIQR IRELSIQSSN GIYSAEDRLY IQVEVSQLIA EVDRIASHAQ FNGMNMLTGR FAQETGENTV TASMWFHIGA N MDQRTRAY ...String:
MIINHNMSAM FSQRTLGHTH LLNQKNIEKL SSGLRINRAG DDASGLAVSE KMRSQIRGLN QASANAQNGI SFIQVAEAFL QETTDVIQR IRELSIQSSN GIYSAEDRLY IQVEVSQLIA EVDRIASHAQ FNGMNMLTGR FAQETGENTV TASMWFHIGA N MDQRTRAY IGTMTAKALG VRNIGDESIM TIETPEKANR AIGTLDEAIK KINKQRADLG AYQNRLELTV VGINIAAENL QA SESRIRD VDMAKEMVDY TKNQILTQSG TAMLAQANQA TQSVMTLLR

UniProtKB: Flagellin

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Macromolecule #2: Flagellar filament outer layer protein

MacromoleculeName: Flagellar filament outer layer protein / type: protein_or_peptide / ID: 2 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Treponema denticola ATCC 35405 (bacteria)
Molecular weightTheoretical: 39.334648 KDa
SequenceString: MKKTFILVAM AFLLMGAVAV AEEAIIIDFA LLNADIIADP NGKMTQNRRT VMDYGKVAGA SYTDEQKALM RTSLALEQWD VELNSSAQN PLSVATSTIK EAEVRAEGEK FAGQKLMGVR ILFPEWTNNA NAKIKPGFLI PAYEKMAQVD DQGNLQEPTA E DKASGKSR ...String:
MKKTFILVAM AFLLMGAVAV AEEAIIIDFA LLNADIIADP NGKMTQNRRT VMDYGKVAGA SYTDEQKALM RTSLALEQWD VELNSSAQN PLSVATSTIK EAEVRAEGEK FAGQKLMGVR ILFPEWTNNA NAKIKPGFLI PAYEKMAQVD DQGNLQEPTA E DKASGKSR FEDGYGVVRN TGVIKSIAVN TYGMNFPHGL YVLLRDQNNV VKRYFMGYLL FDGWRELVWN NPSYIANVKS RE LRLYPVY PTALPHVAFE GFLITRDAAH DGGDAIAYFK DVKIIYDKAV LTTVRDFADE DLWGIQEERE TKRKKIEVEK FGH TQVLRF LEQEKMATEE GFTPSEGSEK NQQ

UniProtKB: Flagellar filament outer layer protein

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Macromolecule #3: (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: 3 / Number of copies: 45 / 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: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Software - details: No symmetry applied
Details: This is reconstructed from pseudo-particles following symmetry expansion of 56413 particles by 6 assymmetric units with relion_particle_symmetry_expand: Twist of -33.57 and rise of 23.9.
Number images used: 56413
CTF correctionType: 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 a fasta file containing the amino acids for only the relevant proteins.
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-9pim:
Outer Curvature of Thick Flagellar Filament from T.denticola

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