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- EMDB-63660: the flagellar filament cap FliD in complex with FliC -

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Basic information

Entry
Database: EMDB / ID: EMD-63660
Titlethe flagellar filament cap FliD in complex with FliC
Map data
Sample
  • Complex: the flagellar filament cap FliD in complex with FliC
    • Protein or peptide: Flagellin,Flagellar hook-associated protein 2
KeywordsComplex / STRUCTURAL PROTEIN
Function / homology
Function and homology information


TLR5 cascade / MyD88 cascade initiated on plasma membrane / NFkB and MAPK activation mediated by TRAF6 / bacterial-type flagellum filament cap / The IPAF inflammasome / bacterial-type flagellum hook / bacterial-type flagellum / bacterial-type flagellum-dependent cell motility / cell adhesion / receptor ligand activity ...TLR5 cascade / MyD88 cascade initiated on plasma membrane / NFkB and MAPK activation mediated by TRAF6 / bacterial-type flagellum filament cap / The IPAF inflammasome / bacterial-type flagellum hook / bacterial-type flagellum / bacterial-type flagellum-dependent cell motility / cell adhesion / receptor ligand activity / structural molecule activity / : / extracellular region
Similarity search - Function
Flagellin D3 / : / Flagellin D3 domain / Flagellin, barrel domain / 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 D3 / : / Flagellin D3 domain / Flagellin, barrel domain / 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 / 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
Flagellin / Flagellar hook-associated protein 2
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsXing Q / Cheng XQ / Jiang WX
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)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_63660.png

Downloads & links

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Map

FileDownload / File: emd_63660.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.76 Å/pix.
x 600 pix.
= 456. Å		0.76 Å/pix.
x 600 pix.
= 456. Å		0.76 Å/pix.
x 600 pix.
= 456. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.76 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.60392284 - 1.0112314
Average (Standard dev.)-0.000059962644 (±0.011099577)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 456.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63660_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_63660_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 flagellar filament cap FliD in complex with FliC

EntireName: the flagellar filament cap FliD in complex with FliC
Components
  • Complex: the flagellar filament cap FliD in complex with FliC
    • Protein or peptide: Flagellin,Flagellar hook-associated protein 2

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Supramolecule #1: the flagellar filament cap FliD in complex with FliC

SupramoleculeName: the flagellar filament cap FliD in complex with FliC / 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: Flagellin,Flagellar hook-associated protein 2

MacromoleculeName: Flagellin,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 P06179/P16328.
Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 104.813438 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHHHH HENLYFQGGS MAQVINTNSL SLLTQNNLNK SQSALGTAIE RLSSGLRINS AKDDAAGQAI ANRFTANIKG LTQASRNAN DGISIAQTTE GALNEINNNL QRVRELAVQS ANSTNSQSDL DSIQAEITQR LNEIDRVSGQ TQFNGVKVLA Q DNTLTIQV ...String:
MHHHHHHHHH HENLYFQGGS MAQVINTNSL SLLTQNNLNK SQSALGTAIE RLSSGLRINS AKDDAAGQAI ANRFTANIKG LTQASRNAN DGISIAQTTE GALNEINNNL QRVRELAVQS ANSTNSQSDL DSIQAEITQR LNEIDRVSGQ TQFNGVKVLA Q DNTLTIQV GANDGETIDI DLKQINSQTL GLDTLNVQQK YKVSDTAATV TGYADTTIAL DNSTFKASAT GLGGTDQKID GD LKFDDTT GKYYAKVTVT GGTGKDGYYE VSVDKTNGEV TLAGGATSPL TGGLPATATE DVKNVQVANA DLTEAKAALT AAG VTGTAS VVKMSYTDNN GKTIDGGLAV KVGDDYYSAT QNKDGSISIN TTKYTADDGT SKTALNKLGG ADGKTEVVSI GGKT YAASK AEGHNFKAQP DLAEAAATTT ENPLQKIDAA LAQVDTLRSD LGAVQNRFNS AITNLGNTVN NLTSARSRIE DSDYA TEVS NMSRAQILQQ AGTSVLAQAN QVPQNVLSLL RGSGAGGSEG GMASISSLGV GSNLPLDQLL TDLTKNEKGR LTPITK QQS ANSAKLTAYG TLKSALEKFQ TANTALNKAD LFKSTVASST TEDLKVSTTA GACAGTYKIN VTQLAAAQSL ATKTTFA TT KEQLGDTSVT SRTIKIEQPG RKEPLEIKLD KGDTSMEAIR DAINDADSGI CASIVKVKEN EFQLVLTANS GTDNTMKI T VEGDTKLNDL LAYDSTTNTG NMQELVKAEN AKLNVNGIDI ERQSNTVTDA PQGITLTLTK KVTDATVTVT KDDTKAKEA IKSWVDAYNS LVDTFSSLTK YTAVEPGEEA SDKNGALLGD SVVRTIQTGI RAQFANSGSN SAFKTMAEIG ITQDGTSGKL KIDDDKLTK VLKDNTAAAR ELLVGDGKET GITTKIATEV KSYLADDGII DNAQDNVNAT LKSLTKQYLS VSNSIDETVA R YKAQFTQL DTMMSKLNNT SSYLTQQFTA MNKS

UniProtKB: Flagellin, 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

Concentration4 mg/mL
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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 903918
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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