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- PDB-9nnl: Bordetella filamentous hemagglutinin (FhaB) C-terminal domain bou... -

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Basic information

Entry
Database: PDB / ID: 9nnl
TitleBordetella filamentous hemagglutinin (FhaB) C-terminal domain bound to microtubules
Components
  • Filamentous hemagglutinin/adhesin
  • Tubulin alpha-1B chain
  • Tubulin beta chain
KeywordsTOXIN / microtubule-associated protein
Function / homology
Function and homology information


regulation of actin filament polymerization / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Resolution of Sister Chromatid Cohesion / Hedgehog 'off' state / Cargo trafficking to the periciliary membrane / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Mitotic Prometaphase / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle ...regulation of actin filament polymerization / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Resolution of Sister Chromatid Cohesion / Hedgehog 'off' state / Cargo trafficking to the periciliary membrane / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Mitotic Prometaphase / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / EML4 and NUDC in mitotic spindle formation / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / COPI-mediated anterograde transport / cortical actin cytoskeleton / catalytic activity / microtubule-based process / actin filament / neuron migration / microtubule cytoskeleton organization / structural constituent of cytoskeleton / microtubule cytoskeleton / actin filament binding / mitotic cell cycle / neuron differentiation / microtubule / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / GTPase activity / GTP binding
Similarity search - Function
Filamentous haemagglutinin repeat / Haemagglutinin repeat / Hemagglutinin repeat / Hemagglutinin repeat / Filamentous haemagglutinin FhaB/tRNA nuclease CdiA-like, TPS domain / TPS secretion domain / haemagglutination activity domain / Autotransporter, pectate lyase C-like domain superfamily / Pectin lyase fold / Pectin lyase fold/virulence factor ...Filamentous haemagglutinin repeat / Haemagglutinin repeat / Hemagglutinin repeat / Hemagglutinin repeat / Filamentous haemagglutinin FhaB/tRNA nuclease CdiA-like, TPS domain / TPS secretion domain / haemagglutination activity domain / Autotransporter, pectate lyase C-like domain superfamily / Pectin lyase fold / Pectin lyase fold/virulence factor / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / TAXOL / Filamentous hemagglutinin/adhesin / Tubulin beta chain / Tubulin alpha-1B chain
Similarity search - Component
Biological speciesBordetella bronchiseptica RB50 (bacteria)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.42 Å
AuthorsNeumann, B. / Gonen, S.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)1U24AG079683 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R21AI185695-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM142797 United States
CitationJournal: Science / Year: 2026
Title: Bacteria deliver a microtubule-binding protein into mammalian cells to promote colonization.
Authors: Michael S Costello / Bryan Neumann / Mia W Raimondi / Bonnie J Cuthbert / Jana Holubová / Fernando Garza-Sánchez / Abdul Samad / Ladislav Bumba / Jacob A Torres / Nickolas Holznecht / ...Authors: Michael S Costello / Bryan Neumann / Mia W Raimondi / Bonnie J Cuthbert / Jana Holubová / Fernando Garza-Sánchez / Abdul Samad / Ladislav Bumba / Jacob A Torres / Nickolas Holznecht / Jessica Mendoza / Ondrej Stanek / Sasiprapa Prombhul / Thomas Weimbs / Meghan A Morrissey / Diego Acosta-Alvear / David A Low / Peter Šebo / Celia W Goulding / Shane Gonen / Christopher S Hayes /
Abstract: Pathogenic bacteria use protein adhesins to infect the ciliated respiratory epithelia of vertebrate hosts. In this work, we show that the filamentous hemagglutinin FhaB adhesin of carries a C- ...Pathogenic bacteria use protein adhesins to infect the ciliated respiratory epithelia of vertebrate hosts. In this work, we show that the filamentous hemagglutinin FhaB adhesin of carries a C-terminal microtubule-binding domain (FhaB-CT), which is translocated into host cells to promote colonization. FhaB-CT delivery is required to occupy a niche at the base of cilia in airway epithelia, and mutant bacteria lacking this domain are defective for nasal colonization. These observations suggest that FhaB-CT is transferred into motile respiratory cilia to interact with core axonemal microtubules. We propose that adheres initially to the tips of cilia and then deploys multiple FhaB adhesins to migrate to the base of the cilia forest, where the bacteria resist removal by the mucociliary "escalator" that normally clears the respiratory tract of microbes.
History
DepositionMar 5, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Tubulin beta chain
C: Filamentous hemagglutinin/adhesin
D: Tubulin beta chain
F: Tubulin beta chain
G: Filamentous hemagglutinin/adhesin
H: Tubulin beta chain
A: Tubulin alpha-1B chain
E: Tubulin alpha-1B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)331,67820
Polymers325,3958
Non-polymers6,28312
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 3 types, 8 molecules BDFHCGAE

#1: Protein
Tubulin beta chain / Beta-tubulin


Mass: 49907.770 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: brain / References: UniProt: P02554
#2: Protein Filamentous hemagglutinin/adhesin


Mass: 12677.450 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica RB50 (bacteria)
Gene: fhaB, BB2993 / Plasmid: pCH1166 / Production host: Escherichia coli (E. coli) / Strain (production host): CH2016 / References: UniProt: A0A0H3LWR4
#3: Protein Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 50204.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: brain / References: UniProt: Q2XVP4

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Non-polymers , 5 types, 271 molecules

#4: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Chemical
ChemComp-TA1 / TAXOL


Mass: 853.906 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C47H51NO14 / Comment: medication, chemotherapy, alkaloid*YM
#6: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Bordetella filamentous hemagglutinin (FhaB) C-terminal domain bound to microtubulesCOMPLEX#1-#30MULTIPLE SOURCES
2MicrotubuleCOMPLEX#1, #31NATURAL
3Bordetella filamentous hemagglutinin (FhaB) C-terminal domainCOMPLEX#21RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
22299.75 kDa/nmNO
3325.30 kDa/nmNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDOrgan
22Sus scrofa (pig)9823brain
33Bordetella bronchiseptica RB50 (bacteria)257310
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: CH2016 / Plasmid: pCH1166
Buffer solutionpH: 7.5
SpecimenConc.: 0.83 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: positively glow discharged / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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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: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 20436
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 6 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.3.1particle selection
2SerialEMimage acquisition
4cryoSPARC4.3.1CTF correction
7UCSF ChimeraX1.9model fitting
9cryoSPARC4.3.1initial Euler assignment
12cryoSPARC4.4.13D reconstruction
13PHENIX1.21.2_5419:model refinement
14Coot0.9.8.95model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -0.531 ° / Axial rise/subunit: 82 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 2197679
3D reconstructionResolution: 2.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1193804 / Symmetry type: HELICAL
Atomic model building

3D fitting-ID: 1

IDPDB-IDPdb chain-IDAccession codeChain-IDDetails (eV)Initial refinement model-IDSource nameType
17TQY

7tqy

A7TQYAThe initial model consisted of chain A for PDB entry 7TQY.1PDBexperimental model
27TQY

7tqy

B7TQYBThe initial model consisted of chain B for PDB entry 7TQY.1PDBexperimental model
3AlphaFoldin silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00323002
ELECTRON MICROSCOPYf_angle_d0.52631264
ELECTRON MICROSCOPYf_dihedral_angle_d9.8443562
ELECTRON MICROSCOPYf_chiral_restr0.0413412
ELECTRON MICROSCOPYf_plane_restr0.0044070

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