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- EMDB-63661: the flagellar filament cap FliD in complex with FlgL -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-63661
Titlethe flagellar filament cap FliD in complex with FlgL
Map data
Sample
  • Complex: FliD with FlgL
    • Protein or peptide: Flagellar hook-associated protein 2
    • Protein or peptide: Flagellar hook-associated protein 3
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 / structural molecule activity / extracellular region
Similarity search - Function
Flagellar hook-associated protein 3 / 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 / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region
Similarity search - Domain/homology
Flagellar hook-associated protein 3 / 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_63661.png

Downloads & links

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Map

FileDownload / File: emd_63661.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.)
0.57 Å/pix.
x 600 pix.
= 340.02 Å		0.57 Å/pix.
x 600 pix.
= 340.02 Å		0.57 Å/pix.
x 600 pix.
= 340.02 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.5667 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.5117904 - 0.8563884
Average (Standard dev.)-0.000100470876 (±0.01104626)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 340.02 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63661_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_63661_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 : FliD with FlgL

EntireName: FliD with FlgL
Components
  • Complex: FliD with FlgL
    • Protein or peptide: Flagellar hook-associated protein 2
    • Protein or peptide: Flagellar hook-associated protein 3

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Supramolecule #1: FliD with FlgL

SupramoleculeName: FliD with FlgL / 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: 44.168105 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: LTDLTKNEKG RLTPITKQQS ANSAKLTAYG TLKSALEKFQ TANTALNKAD LFKSTVASST TEDLKVSTTA GAAAGTYKIN VTQLAAAQS LATKTTFATT KEQLGDTSVT SRTIKIEQPG RKEPLEIKLD KGDTSMEAIR DAINDADSGI AASIVKVKEN E FQLVLTAN ...String:
LTDLTKNEKG RLTPITKQQS ANSAKLTAYG TLKSALEKFQ TANTALNKAD LFKSTVASST TEDLKVSTTA GAAAGTYKIN VTQLAAAQS LATKTTFATT KEQLGDTSVT SRTIKIEQPG RKEPLEIKLD KGDTSMEAIR DAINDADSGI AASIVKVKEN E FQLVLTAN SGTDNTMKIT VEGDTKLNDL LAYDSTTNTG NMQELVKAEN AKLNVNGIDI ERQSNTVTDA PQGITLTLTK KV TDATVTV TKDDTKAKEA IKSWVDAYNS LVDTFSSLTK YTAVEPGEEA SDKNGALLGD SVVRTIQTGI RAQFANSGSN SAF KTMAEI GITQDGTSGK LKIDDDKLTK VLKDNTAAAR ELLVGDGKET GITTKIATEV KSYLADDGII DNAQDNVNAT LKSL TKQYL SVSNSIDETV

UniProtKB: Flagellar hook-associated protein 2

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Macromolecule #2: Flagellar hook-associated protein 3

MacromoleculeName: Flagellar hook-associated protein 3 / type: protein_or_peptide / ID: 2
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 P16326.
Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 23.633057 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: VLSQAQAQNS QYALARTFAT QKVSLEESVL SQVTTAIQTA QEKIVYAGNG TLSDDDRASL ATDLQGIRDQ LMNLANSTDG NGRYIFAGY KTEAAPFDQA TGGYHGGEKS VTQQVDSART MVIGHTGAQI FNSITSNAVP EPDGSDSEKN LFVMLDTAIA A LKTPVEGN ...String:
VLSQAQAQNS QYALARTFAT QKVSLEESVL SQVTTAIQTA QEKIVYAGNG TLSDDDRASL ATDLQGIRDQ LMNLANSTDG NGRYIFAGY KTEAAPFDQA TGGYHGGEKS VTQQVDSART MVIGHTGAQI FNSITSNAVP EPDGSDSEKN LFVMLDTAIA A LKTPVEGN NVEKEKAAAA IDKTNRGLKN SLNNVLTVRA ELGTQLSELS TLDSLGSDRA LGQKL

UniProtKB: Flagellar hook-associated protein 3

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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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.01) / Number images used: 453039
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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