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

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Basic information

Entry
Database: PDB / ID: 9pil
TitleThin Flagellar Filament from T. denticola
ComponentsFlagellin
KeywordsPROTEIN FIBRIL / flagella / periplasmic flagella / bacterial flagella / filament
Function / homology
Function and homology information


periplasmic flagellum / structural molecule activity
Similarity search - Function
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
Biological speciesTreponema denticola ATCC 35405 (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsTroman, L.A. / Paul, B. / Ghosal, D.
Funding support Australia, 2items
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, L.A. / Paul, B. / Ghosal, D.
History
DepositionJul 10, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Fd: Flagellin
Fe: Flagellin
Ff: Flagellin
Fg: Flagellin
Fh: Flagellin
Fi: Flagellin
Fj: Flagellin
Fk: Flagellin
Fl: Flagellin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)295,12545
Polymers278,7659
Non-polymers16,35936
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1chain "Fl"
d_2ens_1chain "Fe"
d_3ens_1chain "Ff"
d_4ens_1chain "Fg"
d_5ens_1chain "Fh"
d_6ens_1chain "Fi"
d_7ens_1chain "Fj"
d_8ens_1chain "Fk"
d_9ens_1chain "Fd"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLN / End label comp-ID: GLN / Auth seq-ID: 1 - 285 / Label seq-ID: 1 - 285

Dom-IDAuth asym-IDLabel asym-ID
d_1FlI
d_2FeB
d_3FfC
d_4FgD
d_5FhE
d_6FiF
d_7FjG
d_8FkH
d_9FdA

NCS oper:
IDCodeMatrixVector
1given(0.999318302709, 0.0366393087996, -0.00452668997219), (-0.0366440330157, 0.99932791585, -0.000965115085243), (0.00448828650597, 0.0011303333457, 0.999989288758)-6.34366405303, 6.96599370035, 104.411999706
2given(0.416276504323, -0.9092380722, 3.36452888246E-6), (0.90923790081, 0.416276428122, 0.000612471261142), (-0.000558282762824, -0.000251898238408, 0.999999812434)278.571518548, -60.7875812103, 4.94655809548
3given(0.999794621336, 0.0201911926582, -0.00174094392766), (-0.0201907832253, 0.99979611349, 0.000252436157037), (0.00174568595976, -0.000217233290585, 0.999998452694)-3.53579210352, 3.75838179076, 52.4640728559
4given(0.397527438792, -0.917589010796, 0.00153057943244), (0.917587269832, 0.397529856294, 0.00190147225636), (-0.00235322106859, 0.000648552806666, 0.99999702086)283.390794843, -59.0941292085, -47.6247053512
5given(0.435509346977, -0.900184008453, -0.000599685122028), (0.900184007424, 0.435509598139, -0.000377765374585), (0.000601226975652, -0.000375306604744, 0.999999748836)273.32759162, -62.524630824, 57.525222606
6given(0.835602471402, -0.549333905208, 0.000877710242148), (0.549333842954, 0.835602907308, 0.000332088802315), (-0.000915844868764, 0.00020466171638, 0.999999559671)133.058965093, -71.8851263111, -23.8303276688
7given(0.857185542934, -0.515007009563, -0.000851519434812), (0.515006133427, 0.857185837054, -0.00105985198747), (0.00127574160214, 0.000469952069645, 0.999999075814)122.754708995, -69.3508317655, 81.2165792522
8given(0.844430207951, -0.535664685416, -0.000984225081177), (0.535663495096, 0.844430618927, -0.0012449260102), (0.00149797269408, 0.000524039682736, 0.999998740729)129.14024594, -70.8769612807, 28.3762749947

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Components

#1: Protein
Flagellin


Mass: 30973.941 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Treponema denticola ATCC 35405 (bacteria) / Variant: ATCC 35405 / Strain: ATCC 35405 / References: UniProt: Q73MN3
#2: Chemical...
ChemComp-A1CIM / (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


Mass: 454.426 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: C17H30N2O12 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: FlaB3 molecules from the lattice of a thin periplasmic flagellar filament purified from planktonic T. denticola
Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Treponema denticola ATCC 35405 (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Periplasmic flagella purified from planktonic T. denticola
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K / Details: The sample was back blotted

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.67 sec. / Electron dose: 57.7 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7082

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Processing

EM software
IDNameVersionCategory
1crYOLO1.9.9particle selection
2PHENIX1.21.2_5419model refinement
5CTFFIND4.1CTF correction
13RELION53D reconstruction
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: 65.3 ° / Axial rise/subunit: 4.8 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 665964 / Details: Particle picking using crYOLO filament picker.
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 179219 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Details: ModelAngelo 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.
Atomic model buildingDetails: ModelAngelo generated the initial model from the cryo-EM data.
Source name: Other / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 99.08 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001420619
ELECTRON MICROSCOPYf_angle_d0.593827819
ELECTRON MICROSCOPYf_chiral_restr0.03583258
ELECTRON MICROSCOPYf_plane_restr0.00143672
ELECTRON MICROSCOPYf_dihedral_angle_d16.51457992
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2IFlELECTRON MICROSCOPYNCS constraints1.6940130705E-10
ens_1d_3IFlELECTRON MICROSCOPYNCS constraints1.4521621273E-12
ens_1d_4IFlELECTRON MICROSCOPYNCS constraints6.86938021227E-11
ens_1d_5IFlELECTRON MICROSCOPYNCS constraints9.49792746917E-13
ens_1d_6IFlELECTRON MICROSCOPYNCS constraints6.47680644643E-13
ens_1d_7IFlELECTRON MICROSCOPYNCS constraints4.25432173483E-10
ens_1d_8IFlELECTRON MICROSCOPYNCS constraints4.15390565448E-13
ens_1d_9IFlELECTRON MICROSCOPYNCS constraints5.6239497612E-13

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