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

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Entry
Database: PDB / ID: 6rib
TitleCryo-EM reconstruction of Thermus thermophilus bactofilin double helical filaments
Componentsbactofilin
KeywordsPROTEIN FIBRIL / Prokaryotic cytoskeletons
Function / homologyBactofilin A/B / Polymer-forming cytoskeletal / Polymer-forming cytoskeletal protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsDeng, X. / Lowe, J.
Funding support United Kingdom, 2items
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, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)289,12622
Polymers289,12622
Non-polymers00
Water0
1
A: bactofilin
C: bactofilin
D: bactofilin
G: bactofilin
H: bactofilin
K: bactofilin
L: bactofilin
O: bactofilin
P: bactofilin
S: bactofilin
T: bactofilin


Theoretical massNumber of molelcules
Total (without water)144,56311
Polymers144,56311
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
2
B: bactofilin
E: bactofilin
F: bactofilin
I: bactofilin
J: bactofilin
M: bactofilin
N: bactofilin
Q: bactofilin
R: bactofilin
U: bactofilin
V: bactofilin


Theoretical massNumber of molelcules
Total (without water)144,56311
Polymers144,56311
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
bactofilin


Mass: 13142.075 Da / Num. of mol.: 22
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Gene: TTHA1769 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SHG1

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: bactofilin / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 11
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen 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: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 2130

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 4.89 ° / Axial rise/subunit: 57.46 Å / Axial symmetry: C1
3D reconstructionResolution: 4.2 Å / Resolution method: OTHER / Num. of particles: 346000 / Details: FSC: map versus refined atomic model / Symmetry type: HELICAL
Atomic model buildingProtocol: AB INITIO MODEL

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