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- PDB-5w5e: Re-refinement of the pyocin tube structure -

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Basic information

Entry
Database: PDB / ID: 5w5e
TitleRe-refinement of the pyocin tube structure
ComponentsFIIR2 protein
KeywordsSTRUCTURAL PROTEIN / pyocin / bacteriocin
Function / homologyTail tube protein / Phage tail tube protein FII / FIIR2 protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsWang, F. / Zheng, W. / Taylor, N.M. / Guerrero-Ferreira, R.C. / Leiman, P.G. / Egelman, E.H.
Funding support United States, Switzerland, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122510 United States
Swiss National Science Foundation310030_144243 Switzerland
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
DepositionJun 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Data collection / Category: em_software / pdbx_audit_support
Item: _em_software.name / _pdbx_audit_support.funding_organization
Revision 1.2Sep 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 0THIS ENTRY 5W5E REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN EMD-6270, DETERMINED BY P. ...THIS ENTRY 5W5E REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN EMD-6270, DETERMINED BY P.GE, D.SCHOLL, P.G.LEIMAN, X.YU, J.F.MILLER, Z.H.ZHOU

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Structure visualization

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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-6270
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  • EMDB-6270
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Structure viewerMolecule:
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Assembly

Deposited unit
A: FIIR2 protein
B: FIIR2 protein
C: FIIR2 protein
D: FIIR2 protein
E: FIIR2 protein
F: FIIR2 protein
G: FIIR2 protein
H: FIIR2 protein
I: FIIR2 protein
J: FIIR2 protein
K: FIIR2 protein
L: FIIR2 protein
M: FIIR2 protein
N: FIIR2 protein
O: FIIR2 protein
P: FIIR2 protein
Q: FIIR2 protein
R: FIIR2 protein
S: FIIR2 protein
T: FIIR2 protein
U: FIIR2 protein
V: FIIR2 protein
W: FIIR2 protein
X: FIIR2 protein
Y: FIIR2 protein
Z: FIIR2 protein
a: FIIR2 protein
b: FIIR2 protein
c: FIIR2 protein
d: FIIR2 protein


Theoretical massNumber of molelcules
Total (without water)542,65630
Polymers542,65630
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area172410 Å2
ΔGint-927 kcal/mol
Surface area146120 Å2
SymmetryHelical symmetry: (Circular symmetry: 6 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 30 / Rise per n subunits: 38.4 Å / Rotation per n subunits: 18.3 °)
DetailsA helical assembly can be generated by applying the helical parameters to a single subunit, e.g., chain A.

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Components

#1: Protein ...
FIIR2 protein / pyocin tube


Mass: 18088.547 Da / Num. of mol.: 30
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: FIIR2 / Production host: Pseudomonas aeruginosa (bacteria) / References: UniProt: Q9S573

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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 tube of Pseudomonas aeruginosa / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
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 FIELD
Image recordingFilm or detector model: KODAK SO-163 FILM

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Processing

EM software
IDNameCategoryDetails
7RosettaCMmodel fitting
13PHENIXmodel refinementreal_space_refine
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 18.3 ° / Axial rise/subunit: 38.4 Å / Axial symmetry: C6
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50000 / Symmetry type: HELICAL

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