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- EMDB-63662: structure of FliD-FliC at a 10:10 stoichiometry -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-63662
Titlestructure of FliD-FliC at a 10:10 stoichiometry
Map data
Sample
  • Complex: the FliD-FliC with 10:10 stoichiometry
    • Protein or peptide: Flagellar hook-associated protein 2
    • Protein or peptide: Flagellin
KeywordsComplex / STRUCTURAL PROTEIN
Function / homology
Function and homology information


TLR5 cascade / MyD88 cascade initiated on plasma membrane / bacterial-type flagellum filament cap / NFkB and MAPK activation mediated by TRAF6 / 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 / bacterial-type flagellum filament cap / NFkB and MAPK activation mediated by TRAF6 / 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 / Flagellar hook-associated protein 2 / Flagellar hook-associated protein 2 N-terminus / Flagellar hook-associated protein 2 C-terminus / Flagellin D3 / : / Flagellin D3 domain / Flagellin, barrel domain / Flagellin hook, IN motif ...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 D3 / : / 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: 3.27 Å
AuthorsChen LX / Chen XQ / Zhang FF / Jiang WX / Xing Q
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)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) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63662.png

Downloads & links

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Map

FileDownload / File: emd_63662.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.
= 453.336 Å		0.76 Å/pix.
x 600 pix.
= 453.336 Å		0.76 Å/pix.
x 600 pix.
= 453.336 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.75556 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.48392513 - 0.9635129
Average (Standard dev.)-0.00035685077 (±0.011349516)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 453.336 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63662_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_63662_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-FliC with 10:10 stoichiometry

EntireName: the FliD-FliC with 10:10 stoichiometry
Components
  • Complex: the FliD-FliC with 10:10 stoichiometry
    • Protein or peptide: Flagellar hook-associated protein 2
    • Protein or peptide: Flagellin

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Supramolecule #1: the FliD-FliC with 10:10 stoichiometry

SupramoleculeName: the FliD-FliC with 10:10 stoichiometry / 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: 10 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 45.971234 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: DLTKNEKGRL TPITKQQSAN SAKLTAYGTL KSALEKFQTA NTALNKADLF KSTVASSTTE DLKVSTTAGA AAGTYKINVT QLAAAQSLA TKTTFATTKE QLGDTSVTSR TIKIEQPGRK EPLEIKLDKG DTSMEAIRDA INDADSGIAA SIVKVKENEF Q LVLTANSG ...String:
DLTKNEKGRL TPITKQQSAN SAKLTAYGTL KSALEKFQTA NTALNKADLF KSTVASSTTE DLKVSTTAGA AAGTYKINVT QLAAAQSLA TKTTFATTKE QLGDTSVTSR TIKIEQPGRK EPLEIKLDKG DTSMEAIRDA INDADSGIAA SIVKVKENEF Q LVLTANSG TDNTMKITVE GDTKLNDLLA YDSTTNTGNM QELVKAENAK LNVNGIDIER QSNTVTDAPQ GITLTLTKKV TD ATVTVTK DDTKAKEAIK SWVDAYNSLV DTFSSLTKYT AVEPGEEASD KNGALLGDSV VRTIQTGIRA QFANSGSNSA FKT MAEIGI TQDGTSGKLK IDDDKLTKVL KDNTAAAREL LVGDGKETGI TTKIATEVKS YLADDGIIDN AQDNVNATLK SLTK QYLSV SNSIDETVAR YKAQFTQLDT MMSKL

UniProtKB: Flagellar hook-associated protein 2

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Macromolecule #2: Flagellin

MacromoleculeName: Flagellin / 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 P06179.
Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 41.695375 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: FTANIKGLTQ ASRNANDGIS IAQTTEGALN EINNNLQRVR ELAVQSANST NSQSDLDSIQ AEITQRLNEI DRVSGQTQFN GVKVLAQDN TLTIQVGAND GETIDIDLKQ INSQTLGLDT LNVQQKYKVS DTAATVTGYA DTTIALDNST FKASATGLGG T DQKIDGDL ...String:
FTANIKGLTQ ASRNANDGIS IAQTTEGALN EINNNLQRVR ELAVQSANST NSQSDLDSIQ AEITQRLNEI DRVSGQTQFN GVKVLAQDN TLTIQVGAND GETIDIDLKQ INSQTLGLDT LNVQQKYKVS DTAATVTGYA DTTIALDNST FKASATGLGG T DQKIDGDL KFDDTTGKYY AKVTVTGGTG KDGYYEVSVD KTNGEVTLAG GATSPLTGGL PATATEDVKN VQVANADLTE AK AALTAAG VTGTASVVKM SYTDNNGKTI DGGLAVKVGD DYYSATQNKD GSISINTTKY TADDGTSKTA LNKLGGADGK TEV VSIGGK TYAASKAEGH NFKAQPDLAE AAATTTENPL QKIDAALAQV DTLRSDLGAV QNRFNSAITN LGNTVNNLTS ARSR I

UniProtKB: Flagellin

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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: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.01) / Number images used: 395012
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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