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- EMDB-63649: Structure of the flagellar filament in short-length at 3.02 angst... -

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Basic information

Entry
Database: EMDB / ID: EMD-63649
TitleStructure of the flagellar filament in short-length at 3.02 angstroms resolution
Map datadensity map of FliC filament,short
Sample
  • Organelle or cellular component: FliC
    • Protein or peptide: Flagellin
Keywordsflagellum / FliC / fibril / PROTEIN FIBRIL
Function / homology
Function and homology information


TLR5 cascade / MyD88 cascade initiated on plasma membrane / NFkB and MAPK activation mediated by TRAF6 / The IPAF inflammasome / bacterial-type flagellum / receptor ligand activity / structural molecule activity / extracellular space
Similarity search - Function
Flagellin D3 / : / Flagellin D3 domain / Flagellin, barrel domain / 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
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsChen LX / Jiang WX / Cheng XQ / Dong X / Xing Q
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371277 China
National Natural Science Foundation of China (NSFC)32301028 China
CitationJournal: To Be Published
Title: Structure of the flagellar filament in short-length at 3.02 angstroms resolution
Authors: Chen LX / Jiang WX / Cheng XQ / Dong X / Xing Q
History
DepositionMar 6, 2025-
Header (metadata) releaseMar 11, 2026-
Map releaseMar 11, 2026-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63649.png

Downloads & links

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Map

FileDownload / File: emd_63649.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationdensity map of FliC filament,short
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 480 pix.
= 408. Å		0.85 Å/pix.
x 480 pix.
= 408. Å		0.85 Å/pix.
x 480 pix.
= 408. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.28241837 - 0.54774874
Average (Standard dev.)0.0022056224 (±0.030981453)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 408.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: map half A

Fileemd_63649_half_map_1.map
Annotationmap_half_A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: map half B

Fileemd_63649_half_map_2.map
Annotationmap_half_B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : FliC

EntireName: FliC
Components
  • Organelle or cellular component: FliC
    • Protein or peptide: Flagellin

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Supramolecule #1: FliC

SupramoleculeName: FliC / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)

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Macromolecule #1: Flagellin

MacromoleculeName: Flagellin / type: protein_or_peptide / ID: 1 / Number of copies: 44 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Molecular weightTheoretical: 51.654344 KDa
SequenceString: MAQVINTNSL SLLTQNNLNK SQSALGTAIE RLSSGLRINS AKDDAAGQAI ANRFTANIKG LTQASRNAND GISIAQTTEG ALNEINNNL QRVRELAVQS ANSTNSQSDL DSIQAEITQR LNEIDRVSGQ TQFNGVKVLA QDNTLTIQVG ANDGETIDID L KQINSQTL ...String:
MAQVINTNSL SLLTQNNLNK SQSALGTAIE RLSSGLRINS AKDDAAGQAI ANRFTANIKG LTQASRNAND GISIAQTTEG ALNEINNNL QRVRELAVQS ANSTNSQSDL DSIQAEITQR LNEIDRVSGQ TQFNGVKVLA QDNTLTIQVG ANDGETIDID L KQINSQTL GLDTLNVQQK YKVSDTAATV TGYADTTIAL DNSTFKASAT GLGGTDQKID GDLKFDDTTG KYYAKVTVTG GT GKDGYYE VSVDKTNGEV TLAGGATSPL TGGLPATATE DVKNVQVANA DLTEAKAALT AAGVTGTASV VKMSYTDNNG KTI DGGLAV KVGDDYYSAT QNKDGSISIN TTKYTADDGT SKTALNKLGG ADGKTEVVSI GGKTYAASKA EGHNFKAQPD LAEA AATTT ENPLQKIDAA LAQVDTLRSD LGAVQNRFNS AITNLGNTVN NLTSARSRIE DSDYATEVSN MSRAQILQQA GTSVL AQAN QVPQNVLSLL R

UniProtKB: Flagellin

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.4
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: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 498897
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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