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- PDB-10pl: Asymmetric architecture and adaptation of Treponema flagella -

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Basic information

Entry
Database: PDB / ID: 10pl
TitleAsymmetric architecture and adaptation of Treponema flagella
Components
  • (Flagellar filament outer layer protein FlaA, ...) x 4
  • (Flagellin) x 2
  • Flagellar filament outer layer protein
  • HEAT repeat domain-containing protein
KeywordsMOTOR PROTEIN / Treponema / Flagellin / Motility / Supercoil
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 / : / TP_0437 / 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 ...Flagellar filament outer layer protein FlaA, Spirochaetes / : / TP_0437 / 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 / HEAT repeats / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
HEAT repeat domain-containing protein / Flagellar filament outer layer protein / TP-0437 domain-containing protein / Flagellin / Flagellar filament outer layer protein FlaA, putative / Flagellar filament outer layer protein FlaA, putative
Similarity search - Component
Biological speciesTreponema denticola ATCC 35405 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsWang, J. / Kurniyati, K. / Guo, W. / Botting, J.M. / Sindelar, C.V. / Li, C. / Liu, J.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI087946 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI132818 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI078958 United States
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)R01DE023080 United States
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)R01DE034063 United States
CitationJournal: Nat Commun / Year: 2026
Title: Asymmetric architecture and adaptation of Treponema flagella.
Authors: Wang, J. / Kurniyati, K. / Guo, W. / Botting, J.M. / Wu, H. / Sindelar, C.V. / Li, C. / Liu, J.
History
DepositionJan 30, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 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
Ba: Flagellin
Bd: Flagellin
Bc: Flagellin
Bb: Flagellin
Bk: Flagellin
Bj: Flagellin
Bi: Flagellin
Bh: Flagellin
Bg: Flagellin
Bf: Flagellin
Be: Flagellin
F: Flagellin
A: HEAT repeat domain-containing protein
B: Flagellar filament outer layer protein FlaA, putative
C: Flagellar filament outer layer protein FlaA, putative
D: Flagellar filament outer layer protein FlaA, putative
E: Flagellar filament outer layer protein FlaA, putative
Ab: Flagellar filament outer layer protein
Ag: Flagellar filament outer layer protein
Ah: Flagellar filament outer layer protein
Af: Flagellar filament outer layer protein
Ae: Flagellar filament outer layer protein
Ad: Flagellar filament outer layer protein
Ac: Flagellar filament outer layer protein
Aa: Flagellar filament outer layer protein


Theoretical massNumber of molelcules
Total (without water)769,17325
Polymers769,17325
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 4 types, 21 molecules BaBdBcBbBkBjBiBhBgBfBeFAAbAgAhAfAeAdAcAa

#1: Protein
Flagellin


Mass: 31342.555 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Source: (natural) Treponema denticola ATCC 35405 (bacteria) / References: UniProt: Q73MN1
#2: Protein Flagellin


Mass: 12487.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Treponema denticola ATCC 35405 (bacteria) / References: UniProt: Q73MM8
#3: Protein HEAT repeat domain-containing protein


Mass: 21413.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Treponema denticola ATCC 35405 (bacteria) / References: UniProt: Q73K73
#8: Protein
Flagellar filament outer layer protein


Mass: 36868.539 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Treponema denticola ATCC 35405 (bacteria) / References: UniProt: Q73M00

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Flagellar filament outer layer protein FlaA, ... , 4 types, 4 molecules BCDE

#4: Protein Flagellar filament outer layer protein FlaA, putative


Mass: 23017.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Treponema denticola ATCC 35405 (bacteria) / References: UniProt: Q73MU8
#5: Protein Flagellar filament outer layer protein FlaA, putative


Mass: 23751.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Treponema denticola ATCC 35405 (bacteria) / References: UniProt: Q73MU9
#6: Protein Flagellar filament outer layer protein FlaA, putative


Mass: 23693.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Treponema denticola ATCC 35405 (bacteria) / References: UniProt: Q73MU9
#7: Protein Flagellar filament outer layer protein FlaA, putative


Mass: 25093.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Treponema denticola ATCC 35405 (bacteria) / References: UniProt: Q73MU8

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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Flagellar filament of Treponema denticola / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Treponema denticola ATCC 35405 (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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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 defocus max: 2200 nm / Nominal defocus min: 1600 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 70 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21_5207model refinement
5cryoSPARCCTF correction
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 159002 / Symmetry type: POINT
RefinementHighest resolution: 3.44 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00554785
ELECTRON MICROSCOPYf_angle_d1.03873862
ELECTRON MICROSCOPYf_dihedral_angle_d6.7247588
ELECTRON MICROSCOPYf_chiral_restr0.0538162
ELECTRON MICROSCOPYf_plane_restr0.0079759

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