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- PDB-6ria: Bactofilin from Thermus thermophilus, F105R mutant crystal structure -

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Basic information

Entry
Database: PDB / ID: 6ria
TitleBactofilin from Thermus thermophilus, F105R mutant crystal structure
Componentsbactofilin
KeywordsPROTEIN FIBRIL / Prokaryotic cytoskeletons
Function / homologyBactofilin A/B / Polymer-forming cytoskeletal / Polymer-forming cytoskeletal protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.5 Å
AuthorsLowe, J. / Gonzalez Llamazares, A.
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
Revision 1.2May 15, 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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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
W: bactofilin
X: bactofilin
Y: bactofilin
Z: bactofilin
1: bactofilin
2: bactofilin
3: bactofilin
4: bactofilin
5: bactofilin
6: bactofilin


Theoretical massNumber of molelcules
Total (without water)420,54632
Polymers420,54632
Non-polymers00
Water00
1
A: bactofilin
B: bactofilin
C: bactofilin
D: bactofilin
M: bactofilin
N: bactofilin
O: bactofilin
P: bactofilin
Q: bactofilin
R: bactofilin
W: bactofilin
X: bactofilin


Theoretical massNumber of molelcules
Total (without water)157,70512
Polymers157,70512
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: bactofilin
F: bactofilin
G: bactofilin
H: bactofilin
I: bactofilin
J: bactofilin
K: bactofilin
L: bactofilin
S: bactofilin
T: bactofilin
U: bactofilin
V: bactofilin


Theoretical massNumber of molelcules
Total (without water)157,70512
Polymers157,70512
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
Y: bactofilin
Z: bactofilin
1: bactofilin
2: bactofilin
3: bactofilin
4: bactofilin
5: bactofilin
6: bactofilin


Theoretical massNumber of molelcules
Total (without water)105,1378
Polymers105,1378
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)191.866, 244.896, 505.917
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein ...
bactofilin


Mass: 13142.075 Da / Num. of mol.: 32 / Mutation: F105R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: TTHA1769 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SHG1

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 3.7
Details: 6.7-7.3 v/v % 2-propanol, 0.17-0.19 M lithium sulfate, 0.1 M phosphate citrate, pH 3.7 and 0.4 M ammonium acetate as an additive

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 147502 / % possible obs: 99.2 % / Redundancy: 3.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.07 / Net I/σ(I): 7.1
Reflection shellResolution: 3.5→3.69 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.541 / Num. unique obs: 84093 / CC1/2: 0.869 / Rpim(I) all: 0.309 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 3.5→49.887 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 0.77 / Phase error: 35.37
RfactorNum. reflection% reflection
Rfree0.3069 13945 5 %
Rwork0.2828 --
obs0.284 278667 96.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.5→49.887 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21663 0 0 0 21663
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00321791
X-RAY DIFFRACTIONf_angle_d0.68229342
X-RAY DIFFRACTIONf_dihedral_angle_d23.41813373
X-RAY DIFFRACTIONf_chiral_restr0.0513583
X-RAY DIFFRACTIONf_plane_restr0.0033808
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.53980.40664600.39289024X-RAY DIFFRACTION98
3.5398-3.58140.41024040.39719022X-RAY DIFFRACTION98
3.5814-3.62510.37894770.36658935X-RAY DIFFRACTION98
3.6251-3.67090.38114740.35768818X-RAY DIFFRACTION96
3.6709-3.71920.33915050.33028894X-RAY DIFFRACTION97
3.7192-3.77020.34664610.32558958X-RAY DIFFRACTION97
3.7702-3.8240.35164410.32578926X-RAY DIFFRACTION97
3.824-3.88110.34744330.33548801X-RAY DIFFRACTION96
3.8811-3.94170.38125020.34588630X-RAY DIFFRACTION94
3.9417-4.00630.37184820.32998784X-RAY DIFFRACTION96
4.0063-4.07530.33895090.32978852X-RAY DIFFRACTION97
4.0753-4.14940.37164550.338955X-RAY DIFFRACTION97
4.1494-4.22920.35434210.31528860X-RAY DIFFRACTION96
4.2292-4.31540.32114690.28668768X-RAY DIFFRACTION96
4.3154-4.40920.29654600.27548691X-RAY DIFFRACTION95
4.4092-4.51170.28344900.25798896X-RAY DIFFRACTION97
4.5117-4.62450.21644560.20398734X-RAY DIFFRACTION95
4.6245-4.74940.19664440.18178646X-RAY DIFFRACTION94
4.7494-4.88910.2644290.23078961X-RAY DIFFRACTION97
4.8891-5.04670.34265160.30378852X-RAY DIFFRACTION97
5.0467-5.22690.35954290.31778892X-RAY DIFFRACTION96
5.2269-5.43590.27864700.26648800X-RAY DIFFRACTION96
5.4359-5.6830.33375050.28168848X-RAY DIFFRACTION97
5.683-5.98220.32414270.28058834X-RAY DIFFRACTION95
5.9822-6.35630.28555120.27498652X-RAY DIFFRACTION95
6.3563-6.84590.29954630.26248929X-RAY DIFFRACTION97
6.8459-7.53270.31074840.2648853X-RAY DIFFRACTION97
7.5327-8.61790.25214290.27268676X-RAY DIFFRACTION94
8.6179-10.83930.27394570.26848577X-RAY DIFFRACTION93
10.8393-49.89250.30384810.25878654X-RAY DIFFRACTION94

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