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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 / Cilium Assembly / 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 / Cilium Assembly / 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 / actin filament / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / actin filament binding / mitotic cell cycle / microtubule cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / GTPase activity / GTP binding / metal ion binding / cytoplasm
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: To Be Published
Title: Bordetella filamentous hemagglutinin (FhaB) C-terminal domain bound to microtubules
Authors: Neumann, B. / Gonen, S.
History
DepositionMar 5, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
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Revision 1.0Feb 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half 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
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*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-IDDetailsInitial 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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