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- EMDB-49766: Bordetella filamentous hemagglutinin (FhaB) C-terminal domain bou... -

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Basic information

Entry
Database: EMDB / ID: EMD-49766
TitleBordetella filamentous hemagglutinin (FhaB) C-terminal domain bound to microtubules, ab initio
Map data
Sample
  • Complex: Bordetella filamentous hemagglutinin (FhaB) C-terminal domain bound to microtubules
    • Complex: Microtubule
      • Protein or peptide: Tubulin beta chain
      • Protein or peptide: Tubulin alpha-1B chain
    • Complex: Bordetella filamentous hemagglutinin (FhaB) C-terminal domain
      • Protein or peptide: Filamentous hemagglutinin/adhesin
Keywordsmicrotubule-associated protein / TOXIN
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
Filamentous hemagglutinin/adhesin / Tubulin beta chain / Tubulin alpha-1B chain
Similarity search - Component
Biological speciesSus scrofa (pig) / Bordetella bronchiseptica RB50 (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsNeumann B / Gonen S
Funding support United States, 3 items
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 18, 2025-
Header (metadata) releaseFeb 25, 2026-
Map releaseFeb 25, 2026-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49766.png

Downloads & links

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Map

FileDownload / File: emd_49766.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 512 pix.
= 612.352 Å		1.2 Å/pix.
x 512 pix.
= 612.352 Å		1.2 Å/pix.
x 512 pix.
= 612.352 Å

Surface

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Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.196 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.4928857 - 0.9541231
Average (Standard dev.)0.0029762764 (±0.04222707)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 612.352 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49766_msk_1.map
Projections & Slices
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Mask #2

Fileemd_49766_msk_2.map
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Additional map: sharpened

Fileemd_49766_additional_1.map
Annotationsharpened
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Additional map: local filter

Fileemd_49766_additional_2.map
Annotationlocal filter
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Additional map: local res

Fileemd_49766_additional_3.map
Annotationlocal res
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AxesZYX

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Half map: #2

Fileemd_49766_half_map_1.map
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Half map: #1

Fileemd_49766_half_map_2.map
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Sample components

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Entire : Bordetella filamentous hemagglutinin (FhaB) C-terminal domain bou...

EntireName: Bordetella filamentous hemagglutinin (FhaB) C-terminal domain bound to microtubules
Components
  • Complex: Bordetella filamentous hemagglutinin (FhaB) C-terminal domain bound to microtubules
    • Complex: Microtubule
      • Protein or peptide: Tubulin beta chain
      • Protein or peptide: Tubulin alpha-1B chain
    • Complex: Bordetella filamentous hemagglutinin (FhaB) C-terminal domain
      • Protein or peptide: Filamentous hemagglutinin/adhesin

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Supramolecule #1: Bordetella filamentous hemagglutinin (FhaB) C-terminal domain bou...

SupramoleculeName: Bordetella filamentous hemagglutinin (FhaB) C-terminal domain bound to microtubules
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Microtubule

SupramoleculeName: Microtubule / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #3
Source (natural)Organism: Sus scrofa (pig) / Organ: brain
Molecular weightTheoretical: 100.01 kDa/nm

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Supramolecule #3: Bordetella filamentous hemagglutinin (FhaB) C-terminal domain

SupramoleculeName: Bordetella filamentous hemagglutinin (FhaB) C-terminal domain
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Bordetella bronchiseptica RB50 (bacteria)

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Macromolecule #1: Tubulin beta chain

MacromoleculeName: Tubulin beta chain / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig) / Organ: brain
SequenceString: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEAAGNKYV PRAILVDLE PGTMDSVRSG PFGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV V RKESESCD CLQGFQLTHS LGGGTGSGMG TLLISKIREE YPDRIMNTFS ...String:
MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEAAGNKYV PRAILVDLE PGTMDSVRSG PFGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV V RKESESCD CLQGFQLTHS LGGGTGSGMG TLLISKIREE YPDRIMNTFS VVPSPKVSDT VV EPYNATL SVHQLVENTD ETYCIDNEAL YDICFRTLKL TTPTYGDLNH LVSATMSGVT TCL RFPGQL NADLRKLAVN MVPFPRLHFF MPGFAPLTSR GSQQYRALTV PELTQQMFDA KNMM AACDP RHGRYLTVAA VFRGRMSMKE VDEQMLNVQN KNSSYFVEWI PNNVKTAVCD IPPRG LKMS ATFIGNSTAI QELFKRISEQ FTAMFRRKAF LHWYTGEGMD EMEFTEAESN MNDLVS EYQ QYQDATADEQ GEFEEEGEED EA

UniProtKB: Tubulin beta chain

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Macromolecule #2: Filamentous hemagglutinin/adhesin

MacromoleculeName: Filamentous hemagglutinin/adhesin / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Bordetella bronchiseptica RB50 (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAKSHHHHHH TSPLSGRHVV QQQVQVLQRQ ASDINNTKSL PGGKLPKPVT VKLTDENGKP QTYTINRRED LMKLNGKVLS TKTTLGLEQT FRLRVEDIGG KNYRVFYETN K

UniProtKB: Filamentous hemagglutinin/adhesin

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Macromolecule #3: Tubulin alpha-1B chain

MacromoleculeName: Tubulin alpha-1B chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig) / Organ: brain
SequenceString: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVD LEPTVIDEVR TGTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL D RIRKLADQ CTGLQGFLVF HSFGGGTGSG FTSLLMERLS VDYGKKSKLE ...String:
MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVD LEPTVIDEVR TGTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL D RIRKLADQ CTGLQGFLVF HSFGGGTGSG FTSLLMERLS VDYGKKSKLE FSIYPAPQVS TA VVEPYNS ILTTHTTLEH SDCAFMVDNE AIYDICRRNL DIERPTYTNL NRLISQIVSS ITA SLRFDG ALNVDLTEFQ TNLVPYPRIH FPLATYAPVI SAEKAYHEQL SVAEITNACF EPAN QMVKC DPRHGKYMAC CLLYRGDVVP KDVNAAIATI KTKRSIQFVD WCPTGFKVGI NYQPP TVVP GGDLAKVQRA VCMLSNTTAI AEAWARLDHK FDLMYAKRAF VHWYVGEGME EGEFSE ARE DMAALEKDYE EVGVDSVEGE GEEEGEEY

UniProtKB: Tubulin alpha-1B chain

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.83 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: positively glow discharged
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 6 eV
SoftwareName: SerialEM
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 20436 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 81.984 Å
Applied symmetry - Helical parameters - Δ&Phi: -0.609 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3.1) / Number images used: 940421
CTF correctionSoftware - Name: cryoSPARC (ver. 4.3.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Segment selectionNumber selected: 2197679 / Software - Name: cryoSPARC (ver. 4.3.1)
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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