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- PDB-9m6i: structure of the FliD cap -

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Basic information

Entry
Database: PDB / ID: 9m6i
Titlestructure of the FliD cap
ComponentsFlagellar hook-associated protein 2
KeywordsSTRUCTURAL PROTEIN / Complex
Function / homology
Function and homology information


bacterial-type flagellum filament cap / bacterial-type flagellum hook / bacterial-type flagellum-dependent cell motility / cell adhesion / 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 hook, IN motif / Flagellin hook IN motif
Similarity search - Domain/homology
Flagellar hook-associated protein 2
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsXing, Q. / Cheng, X.Q. / Jiang, W.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32371277 China
CitationJournal: Nat Commun / Year: 2025
Title: Ultraweak interactions drive cap-mediated positioning and elongation of the bacterial flagellar filament.
Authors: Lixia Chen / Xiaoqi Cheng / Fangfang Zhang / Xu Dong / Xin Wang / Wenxue Jiang / Lixin Ma / Qiong Xing /
Abstract: The bacterial flagellum, essential for motility and pathogenesis, requires the filament cap (FliD) to polymerize flagellin (FliC). However, the mechanisms governing the transition from the hook ...The bacterial flagellum, essential for motility and pathogenesis, requires the filament cap (FliD) to polymerize flagellin (FliC). However, the mechanisms governing the transition from the hook junction to the filament elongation remain elusive, obscured by stoichiometric mismatches and barely detectable interactions. To resolve this, we deploy solution NMR to characterize ultra-weak interactions, quantify affinities (K ≈ 0.1 mM for junction protein FlgL; 1.65 mM for FliC). These data enable rational complex stabilization for cryo-EM structure determination of Salmonella FliD pentamers complexed with FlgL or FliC, revealing that both substrates engage an identical conserved surface in a 5:5 stoichiometry. Integrating these structures into native flagellar tip densities reveal a 5:11 FliD:FlgL/FliC architecture, where six additional subunits barely detected by NMR dock at secondary sites. Mutations that disrupt or enhance these interfaces impair motility and filament integrity, while disulfide-locked FliD pentamers confirm that cap rigidity is crucial for elongation. These findings support a rotary cap mechanism where ultra-weak binding and structural fidelity of the cap ensure efficient flagellin polymerization. Our study resolves the long-standing paradox of stoichiometric mismatch in flagellar filament biogenesis, providing a blueprint for the assembly of dynamic macromolecular machines.
History
DepositionMar 7, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flagellar hook-associated protein 2
B: Flagellar hook-associated protein 2
C: Flagellar hook-associated protein 2
D: Flagellar hook-associated protein 2
E: Flagellar hook-associated protein 2


Theoretical massNumber of molelcules
Total (without water)249,7595
Polymers249,7595
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-associated protein 2 / HAP2 / Filament cap protein / Flagellar cap protein


Mass: 49951.723 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: Sequence reference for strain 'Salmonella enterica subsp. enterica serovar Typhimurium' is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id P16328.
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: fliD, flaV, flbC, STM1960 / Production host: Escherichia coli (E. coli) / References: UniProt: P16328
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: the FliD cap / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
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: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.19.2_4158 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 653407 / Symmetry type: POINT
RefinementHighest resolution: 3.06 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00213990
ELECTRON MICROSCOPYf_angle_d0.4818945
ELECTRON MICROSCOPYf_dihedral_angle_d4.5411935
ELECTRON MICROSCOPYf_chiral_restr0.0392390
ELECTRON MICROSCOPYf_plane_restr0.0032435

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