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

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Basic information

Entry
Database: PDB / ID: 9pim
TitleOuter Curvature of Thick Flagellar Filament from T.denticola
Components
  • Flagellar filament outer layer protein
  • Flagellin
KeywordsPROTEIN FIBRIL / flagella / periplasmic flagella / bacterial flagella / filament
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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.7 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: Structural basis of biofilm formation by the oral pathogen Treponema denticola
Authors: Troman, L.A. / Paul, B.
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
CJ: Flagellin
CK: Flagellin
CL: Flagellin
CM: Flagellin
CN: Flagellin
CO: Flagellin
CP: Flagellin
CQ: Flagellin
CR: Flagellin
BR: Flagellar filament outer layer protein
BS: Flagellar filament outer layer protein
BT: Flagellar filament outer layer protein
BU: Flagellar filament outer layer protein
BV: Flagellar filament outer layer protein
BW: Flagellar filament outer layer protein
BX: Flagellar filament outer layer protein
BY: Flagellar filament outer layer protein
BZ: Flagellar filament outer layer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)658,84963
Polymers638,40018
Non-polymers20,44945
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 "BV"
d_2ens_1chain "BS"
d_3ens_1chain "BT"
d_4ens_1chain "BU"
d_5ens_1chain "BR"
d_6ens_1chain "BW"
d_7ens_1chain "BX"
d_8ens_1chain "BY"
d_9ens_1chain "BZ"
d_1ens_2chain "CN"
d_2ens_2chain "CK"
d_3ens_2chain "CL"
d_4ens_2chain "CM"
d_5ens_2chain "CJ"
d_6ens_2chain "CO"
d_7ens_2chain "CP"
d_8ens_2chain "CQ"
d_9ens_2chain "CR"

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1GLUGLUSERSERBVN22 - 34422 - 344
d_2ens_1GLUGLUSERSERBSK22 - 34422 - 344
d_3ens_1GLUGLUSERSERBTL22 - 34422 - 344
d_4ens_1GLUGLUSERSERBUM22 - 34422 - 344
d_5ens_1GLUGLUSERSERBRJ22 - 34422 - 344
d_6ens_1GLUGLUSERSERBWO22 - 34422 - 344
d_7ens_1GLUGLUSERSERBXP22 - 34422 - 344
d_8ens_1GLUGLUSERSERBYQ22 - 34422 - 344
d_9ens_1GLUGLUSERSERBZR22 - 34422 - 344
d_1ens_2METMETARGARGCNE1 - 2861 - 286
d_2ens_2METMETARGARGCKB1 - 2861 - 286
d_3ens_2METMETARGARGCLC1 - 2861 - 286
d_4ens_2METMETARGARGCMD1 - 2861 - 286
d_5ens_2METMETARGARGCJA1 - 2861 - 286
d_6ens_2METMETARGARGCOF1 - 2861 - 286
d_7ens_2METMETARGARGCPG1 - 2861 - 286
d_8ens_2METMETARGARGCQH1 - 2861 - 286
d_9ens_2METMETARGARGCRI1 - 2861 - 286

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.849889119235, -0.526889429486, -0.00871860658698), (0.526695833544, 0.849869639321, -0.0176944931381), (0.01673272043, 0.0104463034248, 0.999805426476)129.305741979, -67.8497087624, 23.5208383974
2given(0.865395526852, -0.50097603946, -0.0106578605825), (0.50032024876, 0.865049733656, -0.036994688566), (0.0277530320171, 0.0266826945444, 0.999258626696)122.259060455, -64.3877048766, 70.9477091175
3given(0.999307512428, -0.0327685639292, 0.0176271614893), (0.0324411380863, 0.999301472802, 0.0185509842267), (-0.0182227375502, -0.0179662927207, 0.999672518459)2.45426696872, -8.81584613556, -45.2887429673
4given(0.83267470539, -0.553761981719, -0.000708947470051), (0.553758816219, 0.832663952105, 0.00468148747623), (-0.00200211477998, -0.00429074211683, 0.999988790471)135.598688469, -72.621286595, -22.3644610366
5given(0.999442608909, 0.0311831763388, -0.0119197739441), (-0.0313684692456, 0.999384769116, -0.0156876510869), (0.0114232497409, 0.0160528119923, 0.999805889457)-3.41335285164, 7.43009483848, 47.2099909191
6given(0.851874623263, 0.52318964507, 0.0241292671364), (-0.52350453952, 0.851976259769, 0.00891346686352), (-0.0158941292012, -0.0202249371075, 0.999669109544)-75.2289029712, 124.444602, -21.349523087
7given(0.833342797193, 0.552755861465, -0.000860222207155), (-0.552752842721, 0.833341912776, 0.00235611446627), (0.00201921530104, -0.00148796074945, 0.999996854366)-72.6402795366, 134.030102876, 23.6186996449
8given(0.817609545955, 0.575639386812, -0.012406720528), (-0.575766127747, 0.817515680664, -0.0127073997385), (0.00282780878384, 0.0175330607669, 0.999842285202)-72.1390159453, 142.111388465, 72.6173802031
9given(0.834313693672, 0.551281136781, 0.00312550478148), (-0.551280048124, 0.834319289235, -0.0012775567175), (-0.0033119618473, -0.000657145362493, 0.999994299518)-73.0800065759, 134.046604785, 24.7436992061
10given(0.815152384713, 0.579105377106, -0.0127887413157), (-0.579239094623, 0.81505534168, -0.0129174788316), (0.00294295047271, 0.0179374526151, 0.999834779769)-72.2263352587, 143.502192003, 72.5907271803
11given(0.999148850039, -0.0412395313362, 0.000936226727196), (0.0412086096864, 0.998903788654, 0.0222052133427), (-0.00185093301631, -0.0221477327744, 0.999752995484)7.26743054339, -11.2860950781, -48.1501936248
12given(0.852313105715, 0.522844306498, 0.0140071763397), (-0.523015391092, 0.852193301199, 0.0148821393853), (-0.00415577999928, -0.0200102112506, 0.999791138658)-73.5788762036, 123.311834882, -24.0629727883
13given(0.999364456224, 0.0340511808076, -0.010545175298), (-0.0342100781921, 0.99929794998, -0.0152734316717), (0.0100176936741, 0.0156244760088, 0.999827745946)-4.26181039965, 7.99196201973, 47.7907584409
14given(0.832950410203, -0.553341839554, -0.00253431280895), (0.553342235621, 0.832953782034, -0.000606030262652), (0.00244630733943, -0.000897549159595, 0.999996604987)135.567879655, -71.755247807, -24.334507843
15given(0.854480570358, -0.519440500751, -0.0066724104156), (0.519275278129, 0.854431356971, -0.0173274853535), (0.0147017143545, 0.0113411817934, 0.999827603735)126.136225578, -67.3306986394, 23.7725365233
16given(0.872888566262, -0.487618991005, -0.0171251423326), (0.486904365415, 0.872798599529, -0.0338636028696), (0.0314593361077, 0.0212208451973, 0.999279733559)118.32705156, -63.6676332445, 71.510634472

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Components

#1: Protein
Flagellin


Mass: 31598.715 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Treponema denticola ATCC 35405 (bacteria) / References: UniProt: Q73NZ6
#2: Protein
Flagellar filament outer layer protein


Mass: 39334.648 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Treponema denticola ATCC 35405 (bacteria) / References: UniProt: Q73M00
#3: 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.: 45 / 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: FlaA1 region of the outer sheath (located at the outer curvature) of thick flagellar filaments purified from planktonic T. denticola
Type: COMPLEX / Entity ID: #2, #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
IDNameVersionCategoryDetails (eV)
1crYOLO1.9.9particle selection
2PHENIX1.21.2_5419model refinement
13RELION53D reconstructionNo symmetry applied
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: 0 ° / Axial rise/subunit: 0.001 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 665964 / Details: Particle picking using crYOLO filament picker.
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 56413
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.
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 a fasta file containing the ...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 a fasta file containing the amino acids for only the relevant proteins.
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: 79.21 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001244937
ELECTRON MICROSCOPYf_angle_d0.505560777
ELECTRON MICROSCOPYf_chiral_restr0.04026957
ELECTRON MICROSCOPYf_plane_restr0.00247884
ELECTRON MICROSCOPYf_dihedral_angle_d14.645617073
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2NBVELECTRON MICROSCOPYNCS constraints4.22105620033E-12
ens_1d_3NBVELECTRON MICROSCOPYNCS constraints1.08499988587E-11
ens_1d_4NBVELECTRON MICROSCOPYNCS constraints1.14259249412E-12
ens_1d_5NBVELECTRON MICROSCOPYNCS constraints6.34630742704E-13
ens_1d_6NBVELECTRON MICROSCOPYNCS constraints5.96968798261E-12
ens_1d_7NBVELECTRON MICROSCOPYNCS constraints5.1812143024E-13
ens_1d_8NBVELECTRON MICROSCOPYNCS constraints5.5300661586E-13
ens_1d_9NBVELECTRON MICROSCOPYNCS constraints4.29024768913E-13
ens_2d_2ECNELECTRON MICROSCOPYNCS constraints1.85582821277E-11
ens_2d_3ECNELECTRON MICROSCOPYNCS constraints4.70833972433E-11
ens_2d_4ECNELECTRON MICROSCOPYNCS constraints7.74598838475E-13
ens_2d_5ECNELECTRON MICROSCOPYNCS constraints9.98052414907E-12
ens_2d_6ECNELECTRON MICROSCOPYNCS constraints8.07694523041E-13
ens_2d_7ECNELECTRON MICROSCOPYNCS constraints2.87367458195E-13
ens_2d_8ECNELECTRON MICROSCOPYNCS constraints2.06777169494E-12
ens_2d_9ECNELECTRON MICROSCOPYNCS constraints6.22077319296E-13

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