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- EMDB-51486: Salmonella cap-filament complex -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-51486
TitleSalmonella cap-filament complex
Map dataThe EM map of cap-filament complex of Salmonella enterica at its native context
Sample
  • Organelle or cellular component: Flagella
    • Protein or peptide: Flagellin
    • Protein or peptide: Flagellar hook-associated protein 2
KeywordsFliC / FliD / cap / filament / flagella / flagellin / TRANSPORT PROTEIN
Function / homology
Function and homology information


bacterial-type flagellum filament cap / bacterial-type flagellum hook / bacterial-type flagellum / bacterial-type flagellum-dependent cell motility / cell adhesion / structural molecule activity / extracellular region
Similarity search - Function
Flagellar hook-associated protein 2, N-terminal / Flagellar hook-associated protein 2, C-terminal / Flagellar hook-associated protein 2 / Flagellar hook-associated protein 2 N-terminus / Flagellar hook-associated protein 2 C-terminus / Flagellin D3 / : / Flagellin D3 domain / Flagellin, barrel domain / Flagellin hook, IN motif ...Flagellar hook-associated protein 2, N-terminal / Flagellar hook-associated protein 2, C-terminal / Flagellar hook-associated protein 2 / Flagellar hook-associated protein 2 N-terminus / Flagellar hook-associated protein 2 C-terminus / Flagellin D3 / : / Flagellin D3 domain / Flagellin, barrel domain / Flagellin hook, IN motif / Flagellin hook IN motif / Flagellin, C-terminal domain, subdomain 2 / 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 2 / Flagellin
Similarity search - Component
Biological speciesSalmonella enterica (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsQin K / Einenkel R / Erhardt M / Bergeron JRC
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_51486.png

Downloads & links

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Map

FileDownload / File: emd_51486.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe EM map of cap-filament complex of Salmonella enterica 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: 0.16
Minimum - Maximum-0.43511844 - 0.6644776
Average (Standard dev.)0.001279335 (±0.033829737)
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_51486_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 B

Fileemd_51486_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Flagella

EntireName: Flagella
Components
  • Organelle or cellular component: Flagella
    • Protein or peptide: Flagellin
    • Protein or peptide: Flagellar hook-associated protein 2

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Supramolecule #1: Flagella

SupramoleculeName: Flagella / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Salmonella enterica (bacteria)

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Macromolecule #1: Flagellin

MacromoleculeName: Flagellin / type: protein_or_peptide / ID: 1 / Number of copies: 17 / 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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Macromolecule #2: Flagellar hook-associated protein 2

MacromoleculeName: Flagellar hook-associated protein 2 / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica (bacteria)
Molecular weightTheoretical: 49.887594 KDa
SequenceString: MASISSLGVG SNLPLDQLLT DLTKNEKGRL TPITKQQSAN SAKLTAYGTL KSALEKFQTA NTALNKADLF KSTVASSTTE DLKVSTTAG AAAGTYKINV TQLAAAQSLA TKTTFATTKE QLGDTSVTSR TIKIEQPGRK EPLEIKLDKG DTSMEAIRDA I NDADSGIA ...String:
MASISSLGVG SNLPLDQLLT DLTKNEKGRL TPITKQQSAN SAKLTAYGTL KSALEKFQTA NTALNKADLF KSTVASSTTE DLKVSTTAG AAAGTYKINV TQLAAAQSLA TKTTFATTKE QLGDTSVTSR TIKIEQPGRK EPLEIKLDKG DTSMEAIRDA I NDADSGIA ASIVKVKENE FQLVLTANSG TDNTMKITVE GDTKLNDLLA YDSTTNTGNM QELVKAENAK LNVNGIDIER QS NTVTDAP QGITLTLTKK VTDATVTVTK DDTKAKEAIK SWVDAYNSLV DTFSSLTKYT AVEPGEEASD KNGALLGDSV VRT IQTGIR AQFANSGSNS AFKTMAEIGI TQDGTSGKLK IDDDKLTKVL KDNTAAAREL LVGDGKETGI TTKIATEVKS YLAD DGIID NAQDNVNATL KSLTKQYLSV SNSIDETVAR YKAQFTQLDT MMSKLNNTSS YLTQQFTAMN KS

UniProtKB: Flagellar hook-associated protein 2

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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
VitrificationCryogen name: ETHANE

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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 / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.9 µm
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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 15225
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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