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- EMDB-1132: A partial atomic structure for the flagellar hook of Salmonella t... -

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Basic information

Entry
Database: EMDB / ID: EMD-1132
TitleA partial atomic structure for the flagellar hook of Salmonella typhimurium.
Map dataThis is a map of the Salmonell Typhimurium Flagellar hook
Sample
  • Sample: Salmonella typhimurium Flagellar hook
  • Protein or peptide: flagellar hook protein
Function / homology
Function and homology information


bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility
Similarity search - Function
Flagellar hook protein FlgE superfamily / Flagellar hook protein FlgE / Flagellar basal body protein FlaE / Flagellar basal body rod protein, conserved site / Flagellar hook-basal body protein, FlgE/F/G / Flagellar hook-basal body protein, FlgE/F/G-like / Flagella basal body rod proteins signature. / Flagellar basal body rod protein, N-terminal / Flagella basal body rod protein / Flagellar basal-body/hook protein, C-terminal domain / Flagellar basal body rod FlgEFG protein C-terminal
Similarity search - Domain/homology
Flagellar hook protein FlgE / Flagellar hook protein FlgE
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 9.0 Å
AuthorsShaikh TR / Thomas DR / Chen JZ / Samatey FA / Matsunami H / Imada K / Namba K / DeRosier DJ
CitationJournal: Proc Natl Acad Sci U S A / Year: 2005
Title: A partial atomic structure for the flagellar hook of Salmonella typhimurium.
Authors: Tanvir R Shaikh / Dennis R Thomas / James Z Chen / Fadel A Samatey / Hideyuki Matsunami / Katsumi Imada / Keiichi Namba / David J Derosier /
Abstract: The axial proteins of the bacterial flagellum function as a drive shaft, universal joint, and propeller driven by the flagellar rotary motor; they also form the putative protein export channel. The N- ...The axial proteins of the bacterial flagellum function as a drive shaft, universal joint, and propeller driven by the flagellar rotary motor; they also form the putative protein export channel. The N- and C-terminal sequences of the eight axial proteins were predicted to form interlocking alpha-domains generating an axial tube. We report on an approximately 1-nm resolution map of the hook from Salmonella typhimurium, which reveals such a tube made from interdigitated, 1-nm rod-like densities similar to those seen in maps of the filament. Atomic models for the two outer domains of the hook subunit were docked into the corresponding outermost features of the map. The N and C termini of the hook subunit fragment are positioned next to each other and face toward the axis of the hook. The placement of these termini would permit the residues missing in the fragment to form the rod-like features that form the core domain of the hook. We also fit the hook atomic model to an approximately 2-nm resolution map of the hook from Caulobacter crescentus. The hook protein sequence from C. crescentus is largely homologous to that of S. typhimurium except for a large insertion (20 kDa). According to difference maps and our fitting, this insertion is found on the outer surface of the hook, consistent with our modeling of the hook.
History
DepositionDec 22, 2004-
Header (metadata) releaseMay 19, 2005-
Map releaseMay 19, 2005-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 8
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 8
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-2bgy
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1132.gif

Downloads & links

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Map

FileDownload / File: emd_1132.map.gz / Format: CCP4 / Size: 4.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a map of the Salmonell Typhimurium Flagellar hook
Voxel sizeX=Y=Z: 3.18 Å
Density
Contour Level1: 22.199999999999999 / Movie #1: 8
Minimum - Maximum-25.293199999999999 - 52.314900000000002
Average (Standard dev.)-4.01785 (±14.918100000000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions9191141
Spacing9191141
CellA: 289.38 Å / B: 289.38 Å / C: 448.38 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.183.183.18
M x/y/z9191141
origin x/y/z0.0000.0000.000
length x/y/z289.380289.380448.380
α/β/γ90.00090.00090.000
start NX/NY/NZ-90-90-190
NX/NY/NZ180180380
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS9191141
D min/max/mean-25.29352.315-4.018

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Supplemental data

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Sample components

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Entire : Salmonella typhimurium Flagellar hook

EntireName: Salmonella typhimurium Flagellar hook
Components
  • Sample: Salmonella typhimurium Flagellar hook
  • Protein or peptide: flagellar hook protein

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Supramolecule #1000: Salmonella typhimurium Flagellar hook

SupramoleculeName: Salmonella typhimurium Flagellar hook / type: sample / ID: 1000
Details: sample is derived from a polyhook mutant in the hook length controling gene fliK
Oligomeric state: Segment of helix containing 75 hooksubunits
Number unique components: 1
Molecular weightExperimental: 3.1 MDa / Method: amino acid sequence

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Macromolecule #1: flagellar hook protein

MacromoleculeName: flagellar hook protein / type: protein_or_peptide / ID: 1 / Name.synonym: FlgE / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: SJW880

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8 / Details: 10 mM tris, 5 mM EDTA, 0.1% triton X-100
GridDetails: 300 mesh copper grids with holey carbon films
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: gravity plunger. vitrification done in cold room at 4 deg C. Polyhooks are straight at 4 deg.

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 66000
Sample stageSpecimen holder: cryo / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 100 K
Alignment procedureLegacy - Astigmatism: corrected at 300,000
Image recordingDigitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 21 µm / Average electron dose: 10 e/Å2 / Bits/pixel: 8

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Image processing

CTF correctionDetails: corrected averaged layerlines
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: OTHER / Software - Name: BRANDEIS HELICAL PACKAGE
Details: average includes 262 datasets and included 46 layerlines out of 84 collected.
DetailsHook is naturally helical when assembled

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Atomic model buiding 1

Initial modelPDB ID:

1w1g


Chain - Chain ID: A
SoftwareName: RSRef
DetailsPDBEntryID_givenInChain. Protocol: semi-rigid body. Two domains are kept as independent rigid bodies, connected by flexible peptide. Refinement is via simulated annealing molecular dynamics, including the adjacent subunits in the helix.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: correl. coeff.
Output model

PDB-2bgy:
Fit of the x-ray structure of the baterial flagellar hook fragment flge31 into an EM map from the hook of Caulobacter crescentus.

PDB-2bgz:
ATOMIC MODEL OF THE BACTERIAL FLAGELLAR BASED ON DOCKING AN X-RAY DERIVED HOOK STRUCTURE INTO AN EM MAP.

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