+Open data
-Basic information
Entry | Database: PDB / ID: 5kyh | ||||||
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Title | Structure of Iho670 Flagellar-like Filament | ||||||
Components | Iho670 | ||||||
Keywords | CELL ADHESION / immunoglobulin fold / Type IV pili / flagellin | ||||||
Function / homology | Flagellin/pilin, N-terminal / membrane / Archaeal Type IV pilin N-terminal domain-containing protein Function and homology information | ||||||
Biological species | Ignicoccus hospitalis (archaea) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4 Å | ||||||
Authors | Braun, T. / Vos, M. / Kalisman, N. / Sherman, N.E. / Rachel, R. / Wirth, R. / Schroeder, G.F. / Egelman, E.H. | ||||||
Funding support | United States, 1items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5kyh.cif.gz | 844.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kyh.ent.gz | 729.1 KB | Display | PDB format |
PDBx/mmJSON format | 5kyh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kyh_validation.pdf.gz | 975.9 KB | Display | wwPDB validaton report |
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Full document | 5kyh_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5kyh_validation.xml.gz | 160.8 KB | Display | |
Data in CIF | 5kyh_validation.cif.gz | 202.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ky/5kyh ftp://data.pdbj.org/pub/pdb/validation_reports/ky/5kyh | HTTPS FTP |
-Related structure data
Related structure data | 8298MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Symmetry | Helical 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 °) |
-Components
#1: Protein | 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
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: Iho670 filament / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Ignicoccus hospitalis (archaea) |
Buffer solution | pH: 6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Helical symmerty | Angular rotation/subunit: 106.65 ° / Axial rise/subunit: 5.3 Å / Axial symmetry: C1 |
3D reconstruction | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 146696 / Algorithm: BACK PROJECTION / Symmetry type: HELICAL |