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- PDB-3j9r: Atomic structures of a bactericidal contractile nanotube in its p... -

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Entry
Database: PDB / ID: 3j9r
TitleAtomic structures of a bactericidal contractile nanotube in its pre- and post-contraction states
Componentssheath
KeywordsSTRUCTURAL PROTEIN / pyocin / bacteriocin / sheath / tube
Function / homologyTail sheath protein, subtilisin-like domain / Phage tail sheath protein subtilisin-like domain / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain / identical protein binding / Similar to FI genes of P2, phiCTX, and PS17: tail sheath
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsGe, P. / Scholl, D. / Leiman, P.G. / Yu, X. / Miller, J.F. / Zhou, Z.H.
CitationJournal: Nat Struct Mol Biol / Year: 2015
Title: Atomic structures of a bactericidal contractile nanotube in its pre- and postcontraction states.
Authors: Peng Ge / Dean Scholl / Petr G Leiman / Xuekui Yu / Jeff F Miller / Z Hong Zhou /
Abstract: R-type pyocins are representatives of contractile ejection systems, a class of biological nanomachines that includes, among others, the bacterial type VI secretion system (T6SS) and contractile ...R-type pyocins are representatives of contractile ejection systems, a class of biological nanomachines that includes, among others, the bacterial type VI secretion system (T6SS) and contractile bacteriophage tails. We report atomic models of the Pseudomonas aeruginosa precontraction pyocin sheath and tube, and the postcontraction sheath, obtained by cryo-EM at 3.5-Å and 3.9-Å resolutions, respectively. The central channel of the tube is negatively charged, in contrast to the neutral and positive counterparts in T6SSs and phage tails. The sheath is interwoven by long N- and C-terminal extension arms emanating from each subunit, which create an extensive two-dimensional mesh that has the same connectivity in the extended and contracted state of the sheath. We propose that the contraction process draws energy from electrostatic and shape complementarities to insert the inner tube through bacterial cell membranes to eventually kill the bacteria.
History
DepositionFeb 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references
Revision 1.2May 20, 2015Group: Database references
Revision 1.3Jul 18, 2018Group: Author supporting evidence / Data collection / Category: em_single_particle_entity / em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.4Feb 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: sheath
B: sheath
F: sheath
E: sheath
D: sheath
C: sheath
0: sheath
1: sheath
5: sheath
4: sheath
3: sheath
2: sheath
G: sheath
H: sheath
L: sheath
K: sheath
J: sheath
I: sheath
M: sheath
N: sheath
R: sheath
Q: sheath
P: sheath
O: sheath
a: sheath
b: sheath
f: sheath
e: sheath
d: sheath
c: sheath
g: sheath
h: sheath
l: sheath
k: sheath
j: sheath
i: sheath


Theoretical massNumber of molelcules
Total (without water)1,484,90436
Polymers1,484,90436
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryHelical symmetry: (Circular symmetry: 6 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 5 / Rise per n subunits: 16.2 Å / Rotation per n subunits: 33.1 °)

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Components

#1: Protein ...
sheath / Similar to FI genes of P2 / phiCTX / and PS17: tail sheath


Mass: 41247.332 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / Strain: PAO / References: UniProt: Q9S574

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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: Pyocin (post-contraction) sheath / Type: COMPLEX / Details: helical
Buffer solutionName: PBS / pH: 7.4 / Details: PBS
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: baked 1.2/1.3 Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temp: 90 K / Humidity: 100 %
Details: Blot for 4 seconds (blot force 1) before plunging into liquid ethane (FEI VITROBOT MARK IV).
Method: Blot time 4 seconds, blot force 1

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Oct 7, 2009 / Details: Scanned with 9200 ED
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1600 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: 80 K
Image recordingElectron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM / Details: Scanned by Nikon 9200 ED
Image scansNum. digital images: 307
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
2RELION3D reconstruction
CTF correctionDetails: Each particle
Helical symmertyAngular rotation/subunit: 33.1 ° / Axial rise/subunit: 16.2 Å / Axial symmetry: C6
3D reconstructionMethod: RelionList of Walmart brands / Resolution: 3.9 Å / Resolution method: OTHER / Nominal pixel size: 1.104 Å / Actual pixel size: 1.104 Å
Details: Model-Map FSC (Helical Details: Relion-based IHRSR)
Symmetry type: HELICAL
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms103824 0 0 0 103824

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