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- PDB-5kyh: Structure of Iho670 Flagellar-like Filament -

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Basic information

Entry
Database: PDB / ID: 5kyh
TitleStructure of Iho670 Flagellar-like Filament
ComponentsIho670
KeywordsCELL ADHESION / immunoglobulin fold / Type IV pili / flagellin
Function / homologyFlagellin/pilin, N-terminal / membrane / Archaeal Type IV pilin N-terminal domain-containing protein
Function and homology information
Biological speciesIgnicoccus hospitalis (archaea)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4 Å
AuthorsBraun, T. / Vos, M. / Kalisman, N. / Sherman, N.E. / Rachel, R. / Wirth, R. / Schroeder, G.F. / Egelman, E.H.
Funding support United States, 1items
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
DepositionJul 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Sep 21, 2016Group: Database references
Revision 1.3Nov 30, 2016Group: Refinement description
Revision 1.4Sep 27, 2017Group: Author supporting evidence / Data collection / Category: em_image_scans / pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

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Assembly

Deposited unit
A: Iho670
B: Iho670
C: Iho670
D: Iho670
E: Iho670
F: Iho670
G: Iho670
H: Iho670
I: Iho670
J: Iho670
K: Iho670
L: Iho670
M: Iho670
N: Iho670
O: Iho670
P: Iho670
Q: Iho670
R: Iho670
S: Iho670
T: Iho670
U: Iho670


Theoretical massNumber of molelcules
Total (without water)682,95221
Polymers682,95221
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area94300 Å2
ΔGint-610 kcal/mol
Surface area227200 Å2
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 21 / Rise per n subunits: 5.3 Å / Rotation per n subunits: 106.65 °)

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Components

#1: Protein ...
Iho670


Mass: 32521.539 Da / Num. of mol.: 21 / Fragment: UNP residues 8-310
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ignicoccus hospitalis (archaea) / Gene: Igni_0670 / Production host: Ignicoccus hospitalis (archaea) / References: UniProt: A8AAA0

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Iho670 filament / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL
Source (natural)Organism: Ignicoccus hospitalis (archaea)
Buffer solutionpH: 6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 20 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 106.65 ° / Axial rise/subunit: 5.3 Å / Axial symmetry: C1
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 146696 / Algorithm: BACK PROJECTION / Symmetry type: HELICAL

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