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- EMDB-5423: Filaments from Ignicoccus hospitalis Show Diversity of Packing in... -

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Basic information

Entry
Database: EMDB / ID: EMD-5423
TitleFilaments from Ignicoccus hospitalis Show Diversity of Packing in Proteins Containing N-terminal Type IV Pilin Helices
Map dataReconstruction of adhesion filament
Sample
  • Sample: Adhesion filament
  • Organelle or cellular component: Adhesion filament
Keywordshelical polymers / Type IV pili
Function / homologyFlagellin/pilin, N-terminal / membrane / Archaeal Type IV pilin N-terminal domain-containing protein
Function and homology information
Biological speciesIgnicoccus hospitalis (archaea)
Methodhelical reconstruction / cryo EM / Resolution: 7.5 Å
AuthorsYu S / Goforth C / Meyer C / Rachel R / Wirth R / Schroeder G / Egelman EH
CitationJournal: J Mol Biol / Year: 2012
Title: Filaments from Ignicoccus hospitalis show diversity of packing in proteins containing N-terminal type IV pilin helices.
Authors: Xiong Yu / Charles Goforth / Carolin Meyer / Reinhard Rachel / Reinhard Wirth / Gunnar F Schröder / Edward H Egelman /
Abstract: Bacterial motility is driven by the rotation of flagellar filaments that supercoil. The supercoiling involves the switching of coiled-coil protofilaments between two different states. In archaea, the ...Bacterial motility is driven by the rotation of flagellar filaments that supercoil. The supercoiling involves the switching of coiled-coil protofilaments between two different states. In archaea, the flagellar filaments responsible for motility are formed by proteins with distinct homology in their N-terminal portion to bacterial Type IV pilins. The bacterial pilins have a single N-terminal hydrophobic α-helix, not the coiled coil found in flagellin. We have used electron cryo-microscopy to study the adhesion filaments from the archaeon Ignicoccus hospitalis. While I. hospitalis is non-motile, these filaments make transitions between rigid stretches and curved regions and appear morphologically similar to true archaeal flagellar filaments. A resolution of ~7.5Å allows us to unambiguously build a model for the packing of these N-terminal α-helices, and this packing is different from several bacterial Type IV pili whose structure has been analyzed by electron microscopy and modeling. Our results show that the mechanism responsible for the supercoiling of bacterial flagellar filaments cannot apply to archaeal filaments.
History
DepositionMay 21, 2012-
Header (metadata) releaseJun 11, 2012-
Map releaseJun 11, 2012-
UpdateJun 11, 2012-
Current statusJun 11, 2012Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j1r
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j1r
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5423_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5423.map.gz / Format: CCP4 / Size: 10.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of adhesion filament
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 200 pix.
= 250. Å		1.25 Å/pix.
x 120 pix.
= 150. Å		1.25 Å/pix.
x 120 pix.
= 150. 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: 1.25 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.284 / Movie #1: 0.2
Minimum - Maximum-0.21551475 - 0.45967805
Average (Standard dev.)0.08450025 (±0.10978656)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-60-60-100
Dimensions120120200
Spacing120120200
CellA: 150.0 Å / B: 150.0 Å / C: 250.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.251.251.25
M x/y/z120120200
origin x/y/z0.0000.0000.000
length x/y/z150.000150.000250.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-150-1500
NX/NY/NZ301301151
MAP C/R/S123
start NC/NR/NS-60-60-100
NC/NR/NS120120200
D min/max/mean-0.2160.4600.085

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Supplemental data

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Sample components

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Entire : Adhesion filament

EntireName: Adhesion filament
Components
  • Sample: Adhesion filament
  • Organelle or cellular component: Adhesion filament

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Supramolecule #1000: Adhesion filament

SupramoleculeName: Adhesion filament / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Adhesion filament

SupramoleculeName: Adhesion filament / type: organelle_or_cellular_component / ID: 1 / Oligomeric state: helical filament / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Ignicoccus hospitalis (archaea)

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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: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TECNAI F20
DateJan 1, 2011
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON COOLSCAN / Number real images: 17 / Bits/pixel: 14
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.4 µm / Nominal defocus min: 1.7 µm / Nominal magnification: 55000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

DetailsThe filaments were reconstructed using IHRSR.
Final reconstructionApplied symmetry - Helical parameters - Δz: 5.3 Å
Applied symmetry - Helical parameters - Δ&Phi: 106.65 °
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.5 Å / Resolution method: OTHER / Software - Name: Spider, IHRSR
Details: Each image was multiplied by the CTF. The final volume was amplitude-corrected in Fourier space by dividing by the sum of the squared CTFs.

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