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

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ID or keywords:

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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 / bacterial-type flagellum hook / The IPAF inflammasome / 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 / bacterial-type flagellum hook / The IPAF inflammasome / bacterial-type flagellum / bacterial-type flagellum-dependent cell motility / cell adhesion / receptor ligand activity / structural molecule activity / extracellular space / extracellular region
Similarity search - Function
Flagellar hook-associated protein 2, N-terminal / Flagellar hook-associated protein 2, C-terminal / Flagellin D3 / Flagellar hook-associated protein 2 / : / Flagellar hook-associated protein 2 N-terminus / Flagellar hook-associated protein 2 C-terminus / Flagellin D3 domain / Flagellin, barrel domain / Flagellin hook, IN motif ...Flagellar hook-associated protein 2, N-terminal / Flagellar hook-associated protein 2, C-terminal / Flagellin D3 / Flagellar hook-associated protein 2 / : / Flagellar hook-associated protein 2 N-terminus / Flagellar hook-associated protein 2 C-terminus / 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
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: To Be Published
Title: Structural insights into the initiation of bacterial flagellar filament elongation
Authors: Chen LX / Dong X / Zhang FF / Cheng XQ / Wang X / Jiang WX / Ma LX / Xing Q
History
DepositionMar 7, 2025-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing 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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