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- EMDB-63663: structure of the FliD cap -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-63663
Titlestructure of the FliD cap
Map data
Sample
  • Complex: the FliD cap
    • Protein or peptide: Flagellar hook-associated protein 2
KeywordsComplex / STRUCTURAL PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsXing Q / Cheng XQ / Jiang WX
Funding support China, 1 items
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, 2025-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63663.png

Downloads & links

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Map

FileDownload / File: emd_63663.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.57 Å/pix.
x 480 pix.
= 272.16 Å		0.57 Å/pix.
x 480 pix.
= 272.16 Å		0.57 Å/pix.
x 480 pix.
= 272.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.567 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.4847113 - 0.6447141
Average (Standard dev.)-0.00035294512 (±0.010992915)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 272.15997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63663_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63663_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : the FliD cap

EntireName: the FliD cap
Components
  • Complex: the FliD cap
    • Protein or peptide: Flagellar hook-associated protein 2

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Supramolecule #1: the FliD cap

SupramoleculeName: the FliD cap / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

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Macromolecule #1: Flagellar hook-associated protein 2

MacromoleculeName: Flagellar hook-associated protein 2 / type: protein_or_peptide / ID: 1
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.
Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 49.951723 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MASISSLGVG SNLPLDQLLT DLTKNEKGRL TPITKQQSAN SAKLTAYGTL KSALEKFQTA NTALNKADLF KSTVASSTTE DLKVSTTAG ACAGTYKINV TQLAAAQSLA TKTTFATTKE QLGDTSVTSR TIKIEQPGRK EPLEIKLDKG DTSMEAIRDA I NDADSGIC ...String:
MASISSLGVG SNLPLDQLLT DLTKNEKGRL TPITKQQSAN SAKLTAYGTL KSALEKFQTA NTALNKADLF KSTVASSTTE DLKVSTTAG ACAGTYKINV TQLAAAQSLA TKTTFATTKE QLGDTSVTSR TIKIEQPGRK EPLEIKLDKG DTSMEAIRDA I NDADSGIC 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 stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Talos Arctica / 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: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 653407
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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