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- EMDB-51493: Salmonella hook-filament junction complex -

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Basic information

Entry
Database: EMDB / ID: EMD-51493
TitleSalmonella hook-filament junction complex
Map dataSalmonella hook-filament junction at its native context
Sample
  • Complex: Shorten flagella of Salmonella enterica
    • Protein or peptide: Flagellar hook protein FlgE
    • Protein or peptide: Flagellar hook-associated protein 1
    • Protein or peptide: Flagellar hook-associated protein
    • Protein or peptide: Flagellin
KeywordsBacterial flagellum / Hook-filament junction / FlgK / FlgL / Salmonella enterica / TRANSPORT PROTEIN
Function / homology
Function and homology information


bacterial-type flagellum hook / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / structural molecule activity / extracellular region / cytosol
Similarity search - Function
: / Flagellar hook-associated protein 1, D2-like domain / Flagellar hook-associated protein 1 / : / Flagellar hook-associated protein FlgK helical domain / Flagellar hook-associated protein 3 / Flagellin D3 / : / Flagellin D3 domain / Flagellin, barrel domain ...: / Flagellar hook-associated protein 1, D2-like domain / Flagellar hook-associated protein 1 / : / Flagellar hook-associated protein FlgK helical domain / Flagellar hook-associated protein 3 / Flagellin D3 / : / Flagellin D3 domain / Flagellin, barrel domain / Flagellar hook protein FlgE superfamily / Flagellar hook protein FlgE / Flagellar basal body protein FlaE D2 domain / Flagellar hook-basal body protein, FlgE/F/G / Flagellar hook-basal body protein, FlgE/F/G-like / : / Flagellar hook protein FlgE/F/G D1 domain / Flagellar basal body rod protein, conserved site / Flagella basal body rod proteins signature. / Flagellin, C-terminal domain, subdomain 2 / Flagellar basal body rod protein, N-terminal / Flagellar basal-body/hook protein, C-terminal domain / Flagella basal body rod protein / Flagellar basal body rod FlgEFG protein C-terminal / Flagellin, C-terminal domain / Bacterial flagellin C-terminal helical region / Flagellin / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region
Similarity search - Domain/homology
Flagellar hook-associated protein / Flagellar hook protein FlgE / Flagellar hook-associated protein 1 / Flagellin
Similarity search - Component
Biological speciesSalmonella enterica (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsQin K / Einenkel R / Erhardt E / Bergeron JR
Funding support United Kingdom, France, 2 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R009759/2 United Kingdom
Human Frontier Science Program (HFSP)RGY0080/2021 France
CitationJournal: Nat Microbiol / Year: 2025
Title: The structure of the complete extracellular bacterial flagellum reveals the mechanism of flagellin incorporation.
Authors: Rosa Einenkel / Kailin Qin / Julia Schmidt / Natalie S Al-Otaibi / Daniel Mann / Tina Drobnič / Eli J Cohen / Nayim Gonzalez-Rodriguez / Jane Harrowell / Elena Shmakova / Morgan Beeby / ...Authors: Rosa Einenkel / Kailin Qin / Julia Schmidt / Natalie S Al-Otaibi / Daniel Mann / Tina Drobnič / Eli J Cohen / Nayim Gonzalez-Rodriguez / Jane Harrowell / Elena Shmakova / Morgan Beeby / Marc Erhardt / Julien R C Bergeron /
Abstract: The bacterial flagellum is essential for motility, adhesion and colonization in pathogens such as Salmonella enterica and Campylobacter jejuni. Its extracellular structure comprises the hook, hook- ...The bacterial flagellum is essential for motility, adhesion and colonization in pathogens such as Salmonella enterica and Campylobacter jejuni. Its extracellular structure comprises the hook, hook-filament junction, filament and filament cap. Native structures of the hook-filament junction and the cap are lacking, and molecular mechanisms of cap-mediated filament assembly are largely uncharacterized. Here we use cryo-electron microscopy to resolve structures of the complete Salmonella extracellular flagellum including the pentameric FliD cap complex (3.7 Å) and the FlgKL hook-filament junction (2.9 Å), as well as the Campylobacter extracellular flagellum before filament assembly (6.5 Å). This, coupled with structure-guided mutagenesis and functional assays, reveals intermediates of filament assembly, showing that FliD cap protein terminal domain movement and clockwise rotation enable flagellin incorporation and stabilization of the filament. We show that the hook-filament junction acts as a buffer, preventing transfer of mechanical stress to the filament, and reveal the structural basis for the initiation of filament assembly. Collectively, this study provides comprehensive insights into flagellum assembly and how flagellin incorporation is coupled with its secretion.
History
DepositionSep 4, 2024-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51493.png

Downloads & links

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Map

FileDownload / File: emd_51493.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSalmonella hook-filament junction at its native context
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 500 pix.
= 539. Å		1.08 Å/pix.
x 500 pix.
= 539. Å		1.08 Å/pix.
x 500 pix.
= 539. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.078 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.37611037 - 0.7212549
Average (Standard dev.)0.0019064992 (±0.038829487)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 539.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_51493_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_51493_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Shorten flagella of Salmonella enterica

EntireName: Shorten flagella of Salmonella enterica
Components
  • Complex: Shorten flagella of Salmonella enterica
    • Protein or peptide: Flagellar hook protein FlgE
    • Protein or peptide: Flagellar hook-associated protein 1
    • Protein or peptide: Flagellar hook-associated protein
    • Protein or peptide: Flagellin

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Supramolecule #1: Shorten flagella of Salmonella enterica

SupramoleculeName: Shorten flagella of Salmonella enterica / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Salmonella enterica (bacteria)
Molecular weightTheoretical: 1.13 MDa

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Macromolecule #1: Flagellar hook protein FlgE

MacromoleculeName: Flagellar hook protein FlgE / type: protein_or_peptide / ID: 1 / Number of copies: 13 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica (bacteria)
Molecular weightTheoretical: 42.233152 KDa
SequenceString: MSFSQAVSGL NAAATNLDVI GNNIANSATY GFKSGTASFA DMFAGSKVGL GVKVAGITQD FTDGTTTNTG RGLDVAISQN GFFRLVDSN GSVFYSRNGQ FKLDENRNLV NMQGMQLTGY PATGTPPTIQ QGANPAPITI PNTLMAAKST TTASMQINLN S TDPVPSKT ...String:
MSFSQAVSGL NAAATNLDVI GNNIANSATY GFKSGTASFA DMFAGSKVGL GVKVAGITQD FTDGTTTNTG RGLDVAISQN GFFRLVDSN GSVFYSRNGQ FKLDENRNLV NMQGMQLTGY PATGTPPTIQ QGANPAPITI PNTLMAAKST TTASMQINLN S TDPVPSKT PFSVSDADSY NKKGTVTVYD SQGNAHDMNV YFVKTKDNEW AVYTHDSSDP AATAPTTAST TLKFNENGIL ES GGTVNIT TGTINGATAA TFSLSFLNSM QQNTGANNIV ATNQNGYKPG DLVSYQINND GTVVGNYSNE QEQVLGQIVL ANF ANNEGL ASQGDNVWAA TQASGVALLG TAGSGNFGKL TNGALEASNV DLSKELVNMI VAQRNYQSNA QTIKTQDQIL NTLV NLR

UniProtKB: Flagellar hook protein FlgE

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Macromolecule #2: Flagellar hook-associated protein 1

MacromoleculeName: Flagellar hook-associated protein 1 / type: protein_or_peptide / ID: 2 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica (bacteria)
Molecular weightTheoretical: 59.153781 KDa
SequenceString: MSSLINHAMS GLNAAQAALN TVSNNINNYN VAGYTRQTTI LAQANSTLGA GGWIGNGVYV SGVQREYDAF ITNQLRGAQN QSSGLTTRY EQMSKIDNLL ADKSSSLSGS LQSFFTSLQT LVSNAEDPAA RQALIGKAEG LVNQFKTTDQ YLRDQDKQVN I AIGSSVAQ ...String:
MSSLINHAMS GLNAAQAALN TVSNNINNYN VAGYTRQTTI LAQANSTLGA GGWIGNGVYV SGVQREYDAF ITNQLRGAQN QSSGLTTRY EQMSKIDNLL ADKSSSLSGS LQSFFTSLQT LVSNAEDPAA RQALIGKAEG LVNQFKTTDQ YLRDQDKQVN I AIGSSVAQ INNYAKQIAN LNDQISRMTG VGAGASPNDL LDQRDQLVSE LNKIVGVEVS VQDGGTYNLT MANGYTLVQG ST ARQLAAV PSSADPTRTT VAYVDEAAGN IEIPEKLLNT GSLGGLLTFR SQDLDQTRNT LGQLALAFAD AFNAQHTKGY DAD GNKGKD FFSIGSPVVY SNSNNADKTV SLTAKVVDST KVQATDYKIV FDGTDWQVTR TADNTTFTAT KDADGKLEID GLKV TVGTG AQKNDSFLLK PVSNAIVDMN VKVTNEAEIA MASESKLDPD VDTGDSDNRN GQALLDLQNS NVVGGNKTFN DAYAT LVSD VGNKTSTLKT SSTTQANVVK QLYKQQQSVS GVNLDEEYGN LQRYQQYYLA NAQVLQTANA LFDALLNIR

UniProtKB: Flagellar hook-associated protein 1

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Macromolecule #3: Flagellar hook-associated protein

MacromoleculeName: Flagellar hook-associated protein / type: protein_or_peptide / ID: 3 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica (bacteria)
Molecular weightTheoretical: 34.201965 KDa
SequenceString: MRISTQMMYE QNMSGITNSQ AEWMKLGEQM STGKRVTNPS DDPIAASQAV VLSQAQAQNS QYALARTFAT QKVSLEESVL SQVTTAIQT AQEKIVYAGN GTLSDDDRAS LATDLQGIRD QLMNLANSTD GNGRYIFAGY KTEAAPFDQA TGGYHGGEKS V TQQVDSAR ...String:
MRISTQMMYE QNMSGITNSQ AEWMKLGEQM STGKRVTNPS DDPIAASQAV VLSQAQAQNS QYALARTFAT QKVSLEESVL SQVTTAIQT AQEKIVYAGN GTLSDDDRAS LATDLQGIRD QLMNLANSTD GNGRYIFAGY KTEAAPFDQA TGGYHGGEKS V TQQVDSAR TMVIGHTGAQ IFNSITSNAV PEPDGSDSEK NLFVMLDTAI AALKTPVEGN NVEKEKAAAA IDKTNRGLKN SL NNVLTVR AELGTQLSEL STLDSLGSDR ALGQKLQMSN LVDVDWNSVI SSYVMQQAAL QASYKTFTDM QGMSLFQLNR

UniProtKB: Flagellar hook-associated protein

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Macromolecule #4: Flagellin

MacromoleculeName: Flagellin / type: protein_or_peptide / ID: 4 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica (bacteria)
Molecular weightTheoretical: 51.654344 KDa
SequenceString: MAQVINTNSL SLLTQNNLNK SQSALGTAIE RLSSGLRINS AKDDAAGQAI ANRFTANIKG LTQASRNAND GISIAQTTEG ALNEINNNL QRVRELAVQS ANSTNSQSDL DSIQAEITQR LNEIDRVSGQ TQFNGVKVLA QDNTLTIQVG ANDGETIDID L KQINSQTL ...String:
MAQVINTNSL SLLTQNNLNK SQSALGTAIE RLSSGLRINS AKDDAAGQAI ANRFTANIKG LTQASRNAND GISIAQTTEG ALNEINNNL QRVRELAVQS ANSTNSQSDL DSIQAEITQR LNEIDRVSGQ TQFNGVKVLA QDNTLTIQVG ANDGETIDID L KQINSQTL GLDTLNVQQK YKVSDTAATV TGYADTTIAL DNSTFKASAT GLGGTDQKID GDLKFDDTTG KYYAKVTVTG GT GKDGYYE VSVDKTNGEV TLAGGATSPL TGGLPATATE DVKNVQVANA DLTEAKAALT AAGVTGTASV VKMSYTDNNG KTI DGGLAV KVGDDYYSAT QNKDGSISIN TTKYTADDGT SKTALNKLGG ADGKTEVVSI GGKTYAASKA EGHNFKAQPD LAEA AATTT ENPLQKIDAA LAQVDTLRSD LGAVQNRFNS AITNLGNTVN NLTSARSRIE DSDYATEVSN MSRAQILQQA GTSVL AQAN QVPQNVLSLL R

UniProtKB: Flagellin

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 88 % / Chamber temperature: 277 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 43.0 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: 2.7 µm / Nominal defocus min: 0.9 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 65561
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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