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- PDB-9gnz: Salmonella cap-filament complex -

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Basic information

Entry
Database: PDB / ID: 9gnz
TitleSalmonella cap-filament complex
Components
  • Flagellar hook-associated protein 2
  • Flagellin
KeywordsTRANSPORT PROTEIN / FliC / FliD / cap / filament / flagella / flagellin
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsQin, K. / Einenkel, R. / Erhardt, M. / Bergeron, J.R.C.
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
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
P: Flagellin
Q: Flagellin
R: Flagellar hook-associated protein 2
S: Flagellar hook-associated protein 2
T: Flagellar hook-associated protein 2
U: Flagellar hook-associated protein 2
V: Flagellar hook-associated protein 2


Theoretical massNumber of molelcules
Total (without water)1,127,56222
Polymers1,127,56222
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Flagellin


Mass: 51654.344 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Source: (natural) Salmonella enterica (bacteria) / References: UniProt: Q6V2T3
#2: Protein
Flagellar hook-associated protein 2 / HAP2 / Flagellar cap protein


Mass: 49887.594 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Salmonella enterica (bacteria) / References: UniProt: A0A663DCQ9
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: Flagella / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL
Source (natural)Organism: Salmonella enterica (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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
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: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15225 / Symmetry type: POINT

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