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

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Open data


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Basic information

Entry
Database: EMDB / ID: 1641
TitleHelical reconstruction of the bacterial L-type flagella filament
Keywordsbacterial flagellum
SampleS. enterica serovar Typhimurium L-type flagella filament
SourceSalmonella enterica subsp. enterica serovar typhimurium / bacteria
Map dataThis is a cryo-EM map of L-type flagellin including data up to 4 Angstrom resolution.
Methodhelical reconstruction, at 4 A resolution
AuthorsMaki-Yonekura S / Yonekura K / Namba K
CitationNat. Struct. Mol. Biol., 2010, 17, 417-422

Nat. Struct. Mol. Biol., 2010, 17, 417-422 StrPapers
Conformational change of flagellin for polymorphic supercoiling of the flagellar filament.
Saori Maki-Yonekura / Koji Yonekura / Keiichi Namba

DateDeposition: Aug 12, 2009 / Header (metadata) release: Jan 26, 2010 / Map release: Aug 19, 2011 / Last update: Aug 12, 2009

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 550
  • Imaged by UCSF CHIMERA
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  • Surface view colored by height
  • Surface level: 550
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-3a5x
  • Surface level: 550
  • Imaged by UCSF CHIMERA
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Supplemental images

Downloads & links

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Map

Fileemd_1641.map.gz (map file in CCP4 format, 33525 KB)
Projections & slicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
251 pix
1 A/pix
= 251. A
131 pix
1 A/pix
= 261. A
261 pix
1 A/pix
= 131. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1 A
Density
Contour Level:550 (by author), 550 (movie #1):
Minimum - Maximum-948.453 - 2134.49
Average (Standard dev.)4.55795 (60.6009)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions131261251
Origin000
Limit130260250
Spacing131261251
CellA: 131 A / B: 261 A / C: 251 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z111
M x/y/z131261251
origin x/y/z0.0000.0000.000
length x/y/z131.000261.000251.000
alpha/beta/gamma90.00090.00090.000
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
Number of components: 1

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Component #1: protein, Flagella filament

ProteinName: Flagella filament / a.k.a: Flagella filament / Oligomeric Details: Helical assembly / Recombinant expression: No
SourceSpecies: Salmonella enterica subsp. enterica serovar typhimurium / bacteria
Strain: SJW1660
Source (natural)Location in cell: Outside cell

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Experimental details

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Sample preparation

Specimen statefilament
Helical parametersHand: LEFT HANDED
VitrificationInstrument: NONE / Cryogen name: ETHANE

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Electron microscopy imaging

ImagingMicroscope: JEOL 3000SFF
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderHolder: Top entry / Model: JEOL / Temperature: 4 K
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionScanner: OTHER / Sampling size: 5 microns

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionAlgorithm: Helical reconstruction / Software: Handmade / CTF correction: Each filament / Resolution: 4 A / Resolution method: Figure of merit

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Atomic model buiding

Output model

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