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- EMDB-4887: Cryo-EM reconstruction of Thermus thermophilus bactofilin double ... -

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Basic information

Entry
Database: EMDB / ID: EMD-4887
TitleCryo-EM reconstruction of Thermus thermophilus bactofilin double helical filaments
Map dataThermus thermophilus bactofilin double filament
Sample
  • Complex: bactofilin
    • Protein or peptide: bactofilin
KeywordsProkaryotic cytoskeletons / PROTEIN FIBRIL
Function / homologyBactofilin A/B / Polymer-forming cytoskeletal / Polymer-forming cytoskeletal protein
Function and homology information
Biological speciesThermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsDeng X / Lowe J
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Wellcome Trust202754/Z/16/Z United Kingdom
Medical Research Council (United Kingdom)U105184326 United Kingdom
CitationJournal: Nat Microbiol / Year: 2019
Title: The structure of bactofilin filaments reveals their mode of membrane binding and lack of polarity.
Authors: Xian Deng / Andres Gonzalez Llamazares / James M Wagstaff / Victoria L Hale / Giuseppe Cannone / Stephen H McLaughlin / Danguole Kureisaite-Ciziene / Jan Löwe /
Abstract: Bactofilins are small β-helical proteins that form cytoskeletal filaments in a range of bacteria. Bactofilins have diverse functions, from cell stalk formation in Caulobacter crescentus to ...Bactofilins are small β-helical proteins that form cytoskeletal filaments in a range of bacteria. Bactofilins have diverse functions, from cell stalk formation in Caulobacter crescentus to chromosome segregation and motility in Myxococcus xanthus. However, the precise molecular architecture of bactofilin filaments has remained unclear. Here, sequence analysis and electron microscopy results reveal that, in addition to being widely distributed across bacteria and archaea, bactofilins are also present in a few eukaryotic lineages such as the Oomycetes. Electron cryomicroscopy analysis demonstrated that the sole bactofilin from Thermus thermophilus (TtBac) forms constitutive filaments that polymerize through end-to-end association of the β-helical domains. Using a nanobody, we determined the near-atomic filament structure, showing that the filaments are non-polar. A polymerization-impairing mutation enabled crystallization and structure determination, while reaffirming the lack of polarity and the strength of the β-stacking interface. To confirm the generality of the lack of polarity, we performed coevolutionary analysis on a large set of sequences. Finally, we determined that the widely conserved N-terminal disordered tail of TtBac is responsible for direct binding to lipid membranes, both on liposomes and in Escherichia coli cells. Membrane binding is probably a common feature of these widespread but only recently discovered filaments of the prokaryotic cytoskeleton.
History
DepositionApr 23, 2019-
Header (metadata) releaseMay 1, 2019-
Map releaseJul 17, 2019-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 8.3
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 8.3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6rib
  • Surface level: 8.3
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6rib
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4887.png

Downloads & links

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Map

FileDownload / File: emd_4887.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThermus thermophilus bactofilin double filament
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 8.300000000000001 / Movie #1: 8.3
Minimum - Maximum-16.317598 - 37.873336999999999
Average (Standard dev.)-0.000000000000286 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 321.00003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z321.000321.000321.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-16.31837.873-0.000

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Supplemental data

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Sample components

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Entire : bactofilin

EntireName: bactofilin
Components
  • Complex: bactofilin
    • Protein or peptide: bactofilin

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Supramolecule #1: bactofilin

SupramoleculeName: bactofilin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)

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Macromolecule #1: bactofilin

MacromoleculeName: bactofilin / type: protein_or_peptide / ID: 1 / Number of copies: 22 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Molecular weightTheoretical: 13.142075 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGRMLGRKER TLTYLGPDTE VLGDMRAKGQ VRIDGLVRGS VLVEGELEVG PTGRVEGERV EARSVLIHGE VKAELTAEKV VLSKTARFT GQLKAQALEV EAGAVFVGQS VAGEHKALEA PKEA

UniProtKB: Polymer-forming cytoskeletal protein

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 11
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number real images: 2130 / Average electron dose: 40.0 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: 57.46 Å
Applied symmetry - Helical parameters - Δ&Phi: 4.89 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: OTHER / Details: FSC: map versus refined atomic model / Number images used: 346000
Startup modelType of model: OTHER / Details: RELION 3
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-6rib:
Cryo-EM reconstruction of Thermus thermophilus bactofilin double helical filaments

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