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- PDB-5o4u: The flagellin of Pyrococcus furiosus -

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Basic information

Entry
Database: PDB / ID: 5o4u
TitleThe flagellin of Pyrococcus furiosus
ComponentsFlagellin
KeywordsCELL ADHESION / archaellar flagellum glycoprotein helical filament
Function / homologyarchaeal-type flagellum / Flagellin, archaea / Archaebacterial flagellin / Flagellin/pilin, N-terminal / archaeal or bacterial-type flagellum-dependent cell motility / structural molecule activity / Flagellin
Function and homology information
Biological speciesPyrococcus furiosus DSM 3638 (archaea)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsDaum, B. / Vonck, J.
CitationJournal: Elife / Year: 2017
Title: Structure and organisation of the archaellum machinery.
Authors: Bertram Daum / Janet Vonck / Annett Bellack / Paushali Chaudhury / Robert Reichelt / Sonja-Verena Albers / Reinhard Rachel / Werner Kühlbrandt /
Abstract: The archaellum is the macromolecular machinery that Archaea use for propulsion or surface adhesion, enabling them to proliferate and invade new territories. The molecular composition of the ...The archaellum is the macromolecular machinery that Archaea use for propulsion or surface adhesion, enabling them to proliferate and invade new territories. The molecular composition of the archaellum and of the motor that drives it appears to be entirely distinct from that of the functionally equivalent bacterial flagellum and flagellar motor. Yet, the structure of the archaellum machinery is scarcely known. Using combined modes of electron cryo-microscopy (cryoEM), we have solved the structure of the archaellum filament at 4.2 Å resolution and visualise the architecture and organisation of its motor complex . This allows us to build a structural model combining the archaellum and its motor complex, paving the way to a molecular understanding of archaeal swimming motion.
History
DepositionMay 31, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Data collection / Category: em_software
Item: _em_software.fitting_id / _em_software.name / _em_software.version
Revision 1.2Aug 30, 2017Group: Data collection / Category: em_software / Item: _em_software.details / _em_software.name
Revision 1.3Mar 28, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.4Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: em_admin / pdbx_data_processing_status ...em_admin / pdbx_data_processing_status / pdbx_database_proc / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _em_admin.last_update
Revision 1.5Oct 23, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB
Revision 1.6Dec 4, 2019Group: Data collection / Category: em_imaging_optics
Item: _em_imaging_optics.energyfilter_name / _em_imaging_optics.energyfilter_slit_width

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Flagellin
B: Flagellin
C: Flagellin
D: Flagellin
E: Flagellin
F: Flagellin
G: Flagellin
H: Flagellin
I: Flagellin
J: Flagellin
K: Flagellin
L: Flagellin
M: Flagellin
N: Flagellin
O: Flagellin
P: Flagellin


Theoretical massNumber of molelcules
Total (without water)356,53416
Polymers356,53416
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area79060 Å2
ΔGint-619 kcal/mol
Surface area110060 Å2
MethodPISA

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Components

#1: Protein
Flagellin /


Mass: 22283.350 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus DSM 3638 (archaea) / References: UniProt: A0A0B4ZYM1

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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: archaellum / Type: COMPLEX / Details: helical fragment of the archaellum / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.0217 MDa / Experimental value: NO
Source (natural)Organism: Pyrococcus furiosus DSM 3638 (archaea)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Details: blotting for 7-10 seconds

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Electron microscopy imaging

MicroscopyModel: JEOL 3200FSC
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 30000 X / Calibrated magnification: 44642 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 3000 nm / Cs: 4.2 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: JEOL 3200FSC CRYOHOLDER
Image recordingAverage exposure time: 8 sec. / Electron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 297
EM imaging opticsEnergyfilter name: In-column Omega Filter / Energyfilter slit width: 20 eV
Image scansMovie frames/image: 40

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Processing

SoftwareName: PHENIX / Version: dev_2356: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1EMANparticle selectionHelixboxer, 4712 helices selected
2RELION2particle selection74823 overlapping segments
5CTFFIND4CTF correction
8Coot0.8.6model fitting
12RELION2classification
13RELION23D reconstruction
20PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING ONLY
Helical symmertyAngular rotation/subunit: 108 ° / Axial rise/subunit: 5.5 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 74823
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13965 / Symmetry type: HELICAL
Atomic model buildingPDB-ID: 5TFY

5tfy


Pdb chain-ID: A / Details: Some built de novo, some based on 5TFY
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00724896
ELECTRON MICROSCOPYf_angle_d1.16833904
ELECTRON MICROSCOPYf_dihedral_angle_d8.1720192
ELECTRON MICROSCOPYf_chiral_restr0.0784192
ELECTRON MICROSCOPYf_plane_restr0.0074320

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