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- PDB-3j1r: Filaments from Ignicoccus hospitalis Show Diversity of Packing in... -

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Entry
Database: PDB / ID: 3j1r
TitleFilaments from Ignicoccus hospitalis Show Diversity of Packing in Proteins Containing N-terminal Type IV Pilin Helices
Componentsarchaeal adhesion filament core
KeywordsCELL ADHESION / STRUCTURAL PROTEIN / helical polymer / flagellar filament
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: 7.5 Å
AuthorsYu, X. / Goforth, C. / Meyer, C. / Rachel, R. / Wirth, R. / Schroeder, G.F. / Egelman, E.H.
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 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2Jul 18, 2018Group: Author supporting evidence / Data collection / Category: em_single_particle_entity / em_software / Item: _em_software.image_processing_id
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,91721
Polymers56,91721
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
DetailsTHE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR HELICAL SYMMETRY WITH THE FOLLOWING PARAMETERS: ROTATION PER SUBUNIT (TWIST) = 106.65 DEGREES; RISE PER SUBUNIT (HEIGHT) = 5.3 ANGSTROM

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Components

#1: Protein/peptide ...
archaeal adhesion filament core


Mass: 2710.340 Da / Num. of mol.: 21 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Ignicoccus hospitalis (archaea) / References: UniProt: A8AAA0
Sequence detailsTHOUGH THE FULL PROTEIN (UNP RESIDUES 1-310) WAS PRESENT, ONLY RESIDUES 8-33 WERE MODELED.

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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: Adhesion filament / Type: COMPLEX
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Jan 1, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 55000 X / Nominal defocus max: 3400 nm / Nominal defocus min: 1700 nm / Cs: 2 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN
Image recordingFilm or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 17
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1IHRSR3D reconstruction
2SPIDER3D reconstruction
CTF correctionDetails: 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.
Helical symmertyAngular rotation/subunit: 106.65 ° / Axial rise/subunit: 5.3 Å / Axial symmetry: C1
3D reconstructionMethod: IHRSR / Resolution: 7.5 Å / Nominal pixel size: 1.25 Å / Actual pixel size: 1.25 Å / Magnification calibration: TMV / Symmetry type: HELICAL
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms4011 0 0 0 4011

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