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- EMDB-49577: Bordetella filamentous hemagglutinin (FhaB) C-terminal domain bou... -

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Basic information

Entry
Database: EMDB / ID: EMD-49577
TitleBordetella filamentous hemagglutinin (FhaB) C-terminal domain bound to microtubules
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
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: TAXOL
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: water
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: 2.42 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 5, 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_49577.png

Downloads & links

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Map

FileDownload / File: emd_49577.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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.196 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.47602272 - 1.9100697
Average (Standard dev.)0.0068255486 (±0.039624475)
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_49577_msk_1.map
Projections & Slices
AxesZYX

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Mask #2

Fileemd_49577_msk_2.map
Projections & Slices
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Additional map: sharpened map

Fileemd_49577_additional_1.map
Annotationsharpened map
Projections & Slices
AxesZYX

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Additional map: local res

Fileemd_49577_additional_2.map
Annotationlocal res
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: local filter

Fileemd_49577_additional_3.map
Annotationlocal filter
Projections & Slices
AxesZYX

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Histogram

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Half map: #2

Fileemd_49577_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_49577_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
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: TAXOL
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: water

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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: #1-#3

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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: 299.75 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)
Molecular weightTheoretical: 25.30 kDa/nm

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Macromolecule #1: Tubulin beta chain

MacromoleculeName: Tubulin beta chain / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig) / Organ: brain
Molecular weightTheoretical: 49.90777 KDa
SequenceString: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEAAGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKESESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS ...String:
MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEAAGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKESESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS VVPSPKVSDT VVEPYNATLS VHQLVENTDE TYCIDNEALY DICFRTLKLT TPTYGDLNHL VSATMSGVTT CL RFPGQLN ADLRKLAVNM VPFPRLHFFM PGFAPLTSRG SQQYRALTVP ELTQQMFDAK NMMAACDPRH GRYLTVAAVF RGR MSMKEV DEQMLNVQNK NSSYFVEWIP NNVKTAVCDI PPRGLKMSAT FIGNSTAIQE LFKRISEQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QDATADEQGE FEEEGEEDEA

UniProtKB: Tubulin beta chain

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Macromolecule #2: Filamentous hemagglutinin/adhesin

MacromoleculeName: Filamentous hemagglutinin/adhesin / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bordetella bronchiseptica RB50 (bacteria)
Molecular weightTheoretical: 12.67745 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAKSHHHHHH TSPLSGRHVV QQQVQVLQRQ ASDINNTKSL PGGKLPKPVT VKLTDENGKP QTYTINRRED LMKLNGKVLS TKTTLGLEQ TFRLRVEDIG GKNYRVFYET NK

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 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig) / Organ: brain
Molecular weightTheoretical: 50.204445 KDa
SequenceString: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFLVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE ...String:
MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFLVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE FSIYPAPQVS TAVVEPYNSI LTTHTTLEHS DCAFMVDNEA IYDICRRNLD IERPTYTNLN RLISQIVSSI TA SLRFDGA LNVDLTEFQT NLVPYPRIHF PLATYAPVIS AEKAYHEQLS VAEITNACFE PANQMVKCDP RHGKYMACCL LYR GDVVPK DVNAAIATIK TKRSIQFVDW CPTGFKVGIN YQPPTVVPGG DLAKVQRAVC MLSNTTAIAE AWARLDHKFD LMYA KRAFV HWYVGEGMEE GEFSEAREDM AALEKDYEEV GVDSVEGEGE EEGEEY

UniProtKB: Tubulin alpha-1B chain

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Macromolecule #4: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 4 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

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Macromolecule #5: TAXOL

MacromoleculeName: TAXOL / type: ligand / ID: 5 / Number of copies: 4 / Formula: TA1
Molecular weightTheoretical: 853.906 Da
Chemical component information

ChemComp-TA1:
TAXOL / medication, chemotherapy*YM

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Macromolecule #6: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 2 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 259 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 82.0 Å
Applied symmetry - Helical parameters - Δ&Phi: -0.531 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.42 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 1193804
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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Atomic model buiding 1

Initial model
PDB IDChainDetails

7tqy

chain_id: A, source_name: PDB, initial_model_type: experimental modelThe initial model consisted of chain A for PDB entry 7TQY.

7tqy

chain_id: B, source_name: PDB, initial_model_type: experimental modelThe initial model consisted of chain B for PDB entry 7TQY.
source_name: AlphaFold, initial_model_type: in silico model
SoftwareName: UCSF ChimeraX (ver. 1.9)
Output model

PDB-9nnl:
Bordetella filamentous hemagglutinin (FhaB) C-terminal domain bound to microtubules

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