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- EMDB-8298: Structure of Iho670 Flagellar-like Filament -

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Basic information

Entry
Database: EMDB / ID: EMD-8298
TitleStructure of Iho670 Flagellar-like Filament
Map data3D cryo-EM reconstruction of the I. hospitalis Iho670 flagellar-like filament
Sample
  • Organelle or cellular component: Iho670 filament
    • Protein or peptide: Iho670
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: 4.0 Å
AuthorsBraun T / Vos M / Kalisman N / Sherman NE / Rachel R / Wirth R / Schroeder GF / Egelman EH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)EB001567 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2016
Title: Archaeal flagellin combines a bacterial type IV pilin domain with an Ig-like domain.
Authors: Tatjana Braun / Matthijn R Vos / Nir Kalisman / Nicholas E Sherman / Reinhard Rachel / Reinhard Wirth / Gunnar F Schröder / Edward H Egelman /
Abstract: The bacterial flagellar apparatus, which involves ∼40 different proteins, has been a model system for understanding motility and chemotaxis. The bacterial flagellar filament, largely composed of a ...The bacterial flagellar apparatus, which involves ∼40 different proteins, has been a model system for understanding motility and chemotaxis. The bacterial flagellar filament, largely composed of a single protein, flagellin, has been a model for understanding protein assembly. This system has no homology to the eukaryotic flagellum, in which the filament alone, composed of a microtubule-based axoneme, contains more than 400 different proteins. The archaeal flagellar system is simpler still, in some cases having ∼13 different proteins with a single flagellar filament protein. The archaeal flagellar system has no homology to the bacterial one and must have arisen by convergent evolution. However, it has been understood that the N-terminal domain of the archaeal flagellin is a homolog of the N-terminal domain of bacterial type IV pilin, showing once again how proteins can be repurposed in evolution for different functions. Using cryo-EM, we have been able to generate a nearly complete atomic model for a flagellar-like filament of the archaeon Ignicoccus hospitalis from a reconstruction at ∼4-Å resolution. We can now show that the archaeal flagellar filament contains a β-sandwich, previously seen in the FlaF protein that forms the anchor for the archaeal flagellar filament. In contrast to the bacterial flagellar filament, where the outer globular domains make no contact with each other and are not necessary for either assembly or motility, the archaeal flagellin outer domains make extensive contacts with each other that largely determine the interesting mechanical properties of these filaments, allowing these filaments to flex.
History
DepositionAug 23, 2016-
Header (metadata) releaseSep 7, 2016-
Map releaseSep 7, 2016-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.8
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2.8
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5kyh
  • Surface level: 2.8
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5kyh
  • Surface level: 2.8
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8298.png

Downloads & links

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Map

FileDownload / File: emd_8298.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D cryo-EM reconstruction of the I. hospitalis Iho670 flagellar-like filament
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 240 pix.
= 259.2 Å		1.08 Å/pix.
x 240 pix.
= 259.2 Å		1.08 Å/pix.
x 240 pix.
= 259.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.8 / Movie #1: 2.8
Minimum - Maximum-7.6823273 - 15.110338
Average (Standard dev.)-0.1247054500 (±0.95140433)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 259.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z259.200259.200259.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-54-3-120
NX/NY/NZ12323205
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-7.68215.110-0.000

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Supplemental data

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Sample components

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Entire : Iho670 filament

EntireName: Iho670 filament
Components
  • Organelle or cellular component: Iho670 filament
    • Protein or peptide: Iho670

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Supramolecule #1: Iho670 filament

SupramoleculeName: Iho670 filament / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Ignicoccus hospitalis (archaea)

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Macromolecule #1: Iho670

MacromoleculeName: Iho670 / type: protein_or_peptide / ID: 1 / Number of copies: 21 / Enantiomer: LEVO
Source (natural)Organism: Ignicoccus hospitalis (archaea)
Molecular weightTheoretical: 32.521539 KDa
Recombinant expressionOrganism: Ignicoccus hospitalis (archaea)
SequenceString: VSPVIATLLL ILIAVAAAVL LYTWVSGLSA NVAGTQVTGK SLTLIQATWA RPATNVGTTI SKDSFDRSKA VLILSFQPPA QVLQGGQAI TIDAIDVLYQ GRVVCHYDSF PMTADDKYHI GQTIGGLTAF GLVFWGFVGS TLSDFDAHNE TLVPGGIIHG K SDLATQPA ...String:
VSPVIATLLL ILIAVAAAVL LYTWVSGLSA NVAGTQVTGK SLTLIQATWA RPATNVGTTI SKDSFDRSKA VLILSFQPPA QVLQGGQAI TIDAIDVLYQ GRVVCHYDSF PMTADDKYHI GQTIGGLTAF GLVFWGFVGS TLSDFDAHNE TLVPGGIIHG K SDLATQPA ARGYLGGDKG VTGEVHPGEK YKPDILLSFD DQYPFATILA GTWEVNYVST NYVETNFRNT SAVIKFDRFV NT HYSPDTQ NNNGVPIFDV ASASQSNFAV VIWCPNVNPN VMQSVDVKMV FSDGSTWEAS VPLSIT

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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: 6
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 5.3 Å
Applied symmetry - Helical parameters - Δ&Phi: 106.65 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 146696
Startup modelType of model: OTHER / Details: solid cylinder
Final angle assignmentType: NOT APPLICABLE

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