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- PDB-9go6: Salmonella hook-filament junction complex -

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Open data


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Basic information

Entry
Database: PDB / ID: 9go6
TitleSalmonella hook-filament junction complex
Components
  • Flagellar hook protein FlgE
  • Flagellar hook-associated protein
  • Flagellar hook-associated protein 1
  • Flagellin
KeywordsTRANSPORT PROTEIN / Bacterial flagellum / Hook-filament junction / FlgK / FlgL / Salmonella enterica
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsQin, K. / Einenkel, R. / Erhardt, E. / Bergeron, J.R.
Funding support United Kingdom, France, 2items
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, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: Flagellar hook protein FlgE
2: Flagellar hook protein FlgE
3: Flagellar hook protein FlgE
4: Flagellar hook protein FlgE
5: Flagellar hook protein FlgE
6: Flagellar hook protein FlgE
7: Flagellar hook protein FlgE
8: Flagellar hook protein FlgE
9: Flagellar hook protein FlgE
A: Flagellar hook-associated protein 1
B: Flagellar hook-associated protein 1
C: Flagellar hook-associated protein 1
D: Flagellar hook-associated protein 1
E: Flagellar hook-associated protein 1
F: Flagellar hook-associated protein 1
G: Flagellar hook-associated protein 1
H: Flagellar hook-associated protein 1
I: Flagellar hook-associated protein 1
J: Flagellar hook-associated protein 1
K: Flagellar hook-associated protein 1
L: Flagellar hook-associated protein
M: Flagellar hook-associated protein
N: Flagellar hook-associated protein
O: Flagellar hook-associated protein
P: Flagellar hook-associated protein
Q: Flagellar hook-associated protein
R: Flagellar hook-associated protein
S: Flagellar hook-associated protein
T: Flagellar hook-associated protein
U: Flagellar hook-associated protein
V: Flagellar hook-associated protein
a: Flagellin
b: Flagellin
c: Flagellin
d: Flagellin
e: Flagellin
f: Flagellin
g: Flagellin
h: Flagellin
i: Flagellin
j: Flagellin
k: Flagellin
l: Flagellin
m: Flagellin
n: Flagellin
o: Flagellin
w: Flagellar hook protein FlgE
x: Flagellar hook protein FlgE
y: Flagellar hook protein FlgE
z: Flagellar hook protein FlgE


Theoretical massNumber of molelcules
Total (without water)2,350,75950
Polymers2,350,75950
Non-polymers00
Water00
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

#1: Protein
Flagellar hook protein FlgE


Mass: 42233.152 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Source: (natural) Salmonella enterica (bacteria) / References: UniProt: A0A663DET8
#2: Protein
Flagellar hook-associated protein 1 / HAP1


Mass: 59153.781 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Source: (natural) Salmonella enterica (bacteria) / References: UniProt: P0A1J6
#3: Protein
Flagellar hook-associated protein / Flagellar hook-filament junction protein FlgL


Mass: 34201.965 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Source: (natural) Salmonella enterica (bacteria) / References: UniProt: A0A0W3L1H3
#4: Protein
Flagellin


Mass: 51654.344 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Source: (natural) Salmonella enterica (bacteria) / References: UniProt: Q6V2T3
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Shorten flagella of Salmonella enterica / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 1.13 MDa / Experimental value: NO
Source (natural)Organism: Salmonella enterica (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 88 % / 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 defocus max: 2700 nm / Nominal defocus min: 900 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 43 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 65561 / Num. of class averages: 1 / Symmetry type: POINT

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