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- PDB-6u5b: CryoEM Structure of Pyocin R2 - precontracted - baseplate -

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Basic information

Entry
Database: PDB / ID: 6u5b
TitleCryoEM Structure of Pyocin R2 - precontracted - baseplate
Components
  • Glue PA0627
  • Ripcord PA0626
  • Sheath Initiator PA0617
  • Sheath PA0622
  • Tri1a PA0618
  • Tri2 PA0619
  • Tube PA0623
KeywordsANTIMICROBIAL PROTEIN / bacteriocin / pyocin / VIRAL PROTEIN
Function / homology
Function and homology information


Myoviridae, GpU / Uncharacterised protein family, phage P2-GpU-fusion / Phage P2 GpU / Phage Tail Protein X-like / Baseplate assembly protein J, predicted / Phage Tail Protein X / Tail protein I / Phage tail protein (Tail_P2_I) / Tail tube protein / : ...Myoviridae, GpU / Uncharacterised protein family, phage P2-GpU-fusion / Phage P2 GpU / Phage Tail Protein X-like / Baseplate assembly protein J, predicted / Phage Tail Protein X / Tail protein I / Phage tail protein (Tail_P2_I) / Tail tube protein / : / Phage tail tube protein FII / : / Tail sheath protein Gp18 domain III N-terminal region / IraD/Gp25-like / Baseplate wedge protein gp25 / Baseplate protein J-like / Baseplate J-like protein barrel domain / : / 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 / Probable bacteriophage protein / Probable bacteriophage protein / Phage tail protein / Phage tail protein / Probable bacteriophage protein / Probable bacteriophage protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 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-20643
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Structure viewerMolecule:
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Assembly

Deposited unit
m: Tri1a PA0618
M: Sheath PA0622
S: Tube PA0623
0: Tri2 PA0619
a: Sheath Initiator PA0617
6: Glue PA0627
h: Ripcord PA0626
b: Sheath Initiator PA0617
e: Sheath Initiator PA0617
f: Sheath Initiator PA0617
c: Sheath Initiator PA0617
d: Sheath Initiator PA0617
7: Glue PA0627
Y: Glue PA0627
Z: Glue PA0627
8: Glue PA0627
9: Glue PA0627
n: Tri1a PA0618
q: Tri1a PA0618
r: Tri1a PA0618
o: Tri1a PA0618
p: Tri1a PA0618
1: Tri2 PA0619
4: Tri2 PA0619
5: Tri2 PA0619
2: Tri2 PA0619
3: Tri2 PA0619
T: Tube PA0623
W: Tube PA0623
X: Tube PA0623
U: Tube PA0623
V: Tube PA0623
N: Sheath PA0622
Q: Sheath PA0622
R: Sheath PA0622
O: Sheath PA0622
P: Sheath PA0622
g: Ripcord PA0626
l: Ripcord PA0626
k: Ripcord PA0626
j: Ripcord PA0626
i: Ripcord PA0626
s: Tri1a PA0618
A: Sheath PA0622
G: Tube PA0623
B: Sheath PA0622
E: Sheath PA0622
F: Sheath PA0622
C: Sheath PA0622
D: Sheath PA0622
H: Tube PA0623
K: Tube PA0623
L: Tube PA0623
I: Tube PA0623
J: Tube PA0623
t: Tri1a PA0618
w: Tri1a PA0618
x: Tri1a PA0618
u: Tri1a PA0618
v: Tri1a PA0618


Theoretical massNumber of molelcules
Total (without water)1,518,42860
Polymers1,518,42860
Non-polymers00
Water00
1


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

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Components

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Protein , 7 types, 60 molecules mnqropstwxuvMNQROPABEFCDSTWXUV...

#1: Protein
Tri1a PA0618


Mass: 31986.117 Da / Num. of mol.: 12 / 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: G3XCX5
#2: Protein
Sheath PA0622


Mass: 41247.332 Da / Num. of mol.: 12 / 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.: 12 / 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
#4: Protein
Tri2 PA0619


Mass: 20013.682 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: G3XD92
#5: Protein
Sheath Initiator PA0617


Mass: 11862.759 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: G3XD42
#6: Protein
Glue PA0627


Mass: 7486.475 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: G3XD62
#7: Protein
Ripcord PA0626


Mass: 31326.768 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: G3XD65

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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: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22001 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL

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