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- PDB-6u5f: CryoEM Structure of Pyocin R2 - precontracted - collar -

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Basic information

Entry
Database: PDB / ID: 6u5f
TitleCryoEM Structure of Pyocin R2 - precontracted - collar
Components
  • Collar PA0615
  • Sheath PA0622
  • Tube PA0623
KeywordsANTIMICROBIAL PROTEIN / bacteriocin / pyocin
Function / homology
Function and homology information


Tail tube protein / Phage tail tube protein FII / Tail sheath protein Gp18 domain III N-terminal region / Tail sheath protein, subtilisin-like domain / Phage tail sheath protein subtilisin-like domain / : / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain
Similarity search - Domain/homology
Probable bacteriophage protein / Phage protein / Probable bacteriophage protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsGe, P. / Avaylon, J. / Scholl, D. / Shneider, M.M. / Browning, C. / Buth, S.A. / Plattner, M. / Ding, K. / Leiman, P.G. / Miller, J.F. / Zhou, Z.H.
Funding support United States, Switzerland, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM071940 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI085318 United States
Swiss National Science Foundation31003A_146284 Switzerland
National Science Foundation (NSF, United States)XSEDE MCB140140 United States
CitationJournal: Nature / Year: 2020
Title: Action of a minimal contractile bactericidal nanomachine.
Authors: Peng Ge / Dean Scholl / Nikolai S Prokhorov / Jaycob Avaylon / Mikhail M Shneider / Christopher Browning / Sergey A Buth / Michel Plattner / Urmi Chakraborty / Ke Ding / Petr G Leiman / Jeff ...Authors: Peng Ge / Dean Scholl / Nikolai S Prokhorov / Jaycob Avaylon / Mikhail M Shneider / Christopher Browning / Sergey A Buth / Michel Plattner / Urmi Chakraborty / Ke Ding / Petr G Leiman / Jeff F Miller / Z Hong Zhou /
Abstract: R-type bacteriocins are minimal contractile nanomachines that hold promise as precision antibiotics. Each bactericidal complex uses a collar to bridge a hollow tube with a contractile sheath loaded ...R-type bacteriocins are minimal contractile nanomachines that hold promise as precision antibiotics. Each bactericidal complex uses a collar to bridge a hollow tube with a contractile sheath loaded in a metastable state by a baseplate scaffold. Fine-tuning of such nucleic acid-free protein machines for precision medicine calls for an atomic description of the entire complex and contraction mechanism, which is not available from baseplate structures of the (DNA-containing) T4 bacteriophage. Here we report the atomic model of the complete R2 pyocin in its pre-contraction and post-contraction states, each containing 384 subunits of 11 unique atomic models of 10 gene products. Comparison of these structures suggests the following sequence of events during pyocin contraction: tail fibres trigger lateral dissociation of baseplate triplexes; the dissociation then initiates a cascade of events leading to sheath contraction; and this contraction converts chemical energy into mechanical force to drive the iron-tipped tube across the bacterial cell surface, killing the bacterium.
History
DepositionAug 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 20, 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

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  • EMDB-20644
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Assembly

Deposited unit
A: Collar PA0615
G: Sheath PA0622
M: Tube PA0623
H: Sheath PA0622
I: Sheath PA0622
J: Sheath PA0622
K: Sheath PA0622
L: Sheath PA0622
N: Tube PA0623
O: Tube PA0623
P: Tube PA0623
Q: Tube PA0623
R: Tube PA0623
B: Collar PA0615
C: Collar PA0615
D: Collar PA0615
E: Collar PA0615
F: Collar PA0615
S: Sheath PA0622
a: Tube PA0623
0: Tube PA0623
e: Tube PA0623
d: Tube PA0623
m: Tube PA0623
b: Tube PA0623
n: Tube PA0623
1: Tube PA0623
c: Tube PA0623
o: Tube PA0623
2: Tube PA0623
p: Tube PA0623
3: Tube PA0623
q: Tube PA0623
4: Tube PA0623
f: Tube PA0623
r: Tube PA0623
5: Tube PA0623
g: Sheath PA0622
s: Sheath PA0622
T: Sheath PA0622
h: Sheath PA0622
t: Sheath PA0622
U: Sheath PA0622
i: Sheath PA0622
u: Sheath PA0622
V: Sheath PA0622
j: Sheath PA0622
v: Sheath PA0622
W: Sheath PA0622
k: Sheath PA0622
w: Sheath PA0622
X: Sheath PA0622
l: Sheath PA0622
x: Sheath PA0622


Theoretical massNumber of molelcules
Total (without water)1,534,70554
Polymers1,534,70554
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Collar PA0615


Mass: 18965.461 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: G3XD82
#2: Protein ...
Sheath PA0622


Mass: 41247.332 Da / Num. of mol.: 24 / Source method: isolated from a natural source
Source: (natural) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: G3XD39
#3: Protein ...
Tube PA0623


Mass: 17957.352 Da / Num. of mol.: 24 / Source method: isolated from a natural source
Source: (natural) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
References: UniProt: Q9I5S9

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Pyocin R2 / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMTris1
2130 mMSaltNaCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K

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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 FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2160 nm / Nominal defocus min: 2160 nm / Calibrated defocus min: 1100 nm / Calibrated defocus max: 3400 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 81 K / Temperature (min): 80 K
Image recordingAverage exposure time: 10 sec. / Electron dose: 80 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7331
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter upper: 10 eV / Energyfilter lower: -10 eV
Image scansMovie frames/image: 50 / Used frames/image: 3-20

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameVersionCategory
1EMAN1.8particle selection
2Leginon3.2image acquisition
4RELION1.4CTF correction
9PHENIX1.13model refinement
11RELION1.4final Euler assignment
13RELION1.43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 43934
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 4110 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL

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