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- EMDB-1641: Helical reconstruction of the bacterial L-type flagella filament -

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Basic information

Entry
Database: EMDB / ID: EMD-1641
TitleHelical reconstruction of the bacterial L-type flagella filament
Map dataThis is a cryo-EM map of L-type flagellin including data up to 4 Angstrom resolution.
Sample
  • Sample: S. enterica serovar Typhimurium L-type flagella filament
  • Protein or peptide: Flagella filament
Keywordsbacterial flagellum
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 (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsMaki-Yonekura S / Yonekura K / Namba K
CitationJournal: Nat Struct Mol Biol / Year: 2010
Title: Conformational change of flagellin for polymorphic supercoiling of the flagellar filament.
Authors: Saori Maki-Yonekura / Koji Yonekura / Keiichi Namba /
Abstract: The bacterial flagellar filament is a helical propeller rotated by the flagellar motor for bacterial locomotion. The filament is a supercoiled assembly of a single protein, flagellin, and is formed ...The bacterial flagellar filament is a helical propeller rotated by the flagellar motor for bacterial locomotion. The filament is a supercoiled assembly of a single protein, flagellin, and is formed by 11 protofilaments. For bacterial taxis, the reversal of motor rotation switches the supercoil between left- and right-handed, both of which arise from combinations of two distinct conformations and packing interactions of the L-type and R-type protofilaments. Here we report an atomic model of the L-type straight filament by electron cryomicroscopy and helical image analysis. Comparison with the R-type structure shows interesting features: an orientation change of the outer core domains (D1) against the inner core domains (D0) showing almost invariant orientation and packing, a conformational switching within domain D1, and the conformational flexibility of domains D0 and D1 with their spoke-like connection for tight molecular packing.
History
DepositionAug 12, 2009-
Header (metadata) releaseJan 26, 2010-
Map releaseAug 19, 2011-
UpdateOct 10, 2012-
Current statusOct 10, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 550
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 550
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3a5x
  • Surface level: 550
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

em-1641.png

Downloads & links

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Map

FileDownload / File: emd_1641.map.gz / Format: CCP4 / Size: 32 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a cryo-EM map of L-type flagellin including data up to 4 Angstrom resolution.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 251 pix.
= 251. Å		1 Å/pix.
x 131 pix.
= 261. Å		1 Å/pix.
x 261 pix.
= 131. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 550.0 / Movie #1: 550
Minimum - Maximum-948.452999999999975 - 2134.489999999999782
Average (Standard dev.)4.55795 (±60.600900000000003)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions131261251
Spacing131261251
CellA: 131 Å / B: 261 Å / C: 251 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z131261251
origin x/y/z0.0000.0000.000
length x/y/z131.000261.000251.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS261131251
D min/max/mean-948.4532134.4914.558

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Supplemental data

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Sample components

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Entire : S. enterica serovar Typhimurium L-type flagella filament

EntireName: S. enterica serovar Typhimurium L-type flagella filament
Components
  • Sample: S. enterica serovar Typhimurium L-type flagella filament
  • Protein or peptide: Flagella filament

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Supramolecule #1000: S. enterica serovar Typhimurium L-type flagella filament

SupramoleculeName: S. enterica serovar Typhimurium L-type flagella filament
type: sample / ID: 1000 / Number unique components: 1

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Macromolecule #1: Flagella filament

MacromoleculeName: Flagella filament / type: protein_or_peptide / ID: 1 / Name.synonym: Flagella filament / Oligomeric state: Helical assembly / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: SJW1660
synonym: Salmonella enterica subsp. enterica serovar Typhimurium
Location in cell: Outside cell

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

VitrificationCryogen name: ETHANE / Instrument: OTHER

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Electron microscopy

MicroscopeJEOL 3000SFF
TemperatureAverage: 4 K
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 5 µm
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder: Top entry / Specimen holder model: JEOL

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Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: OTHER / Software - Name: Handmade
CTF correctionDetails: Each filament

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