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- PDB-5n8n: Contracted sheath of a Pseudomonas aeruginosa type six secretion ... -

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Basic information

Entry
Database: PDB / ID: 5n8n
TitleContracted sheath of a Pseudomonas aeruginosa type six secretion system consisting of TssB1 and TssC1
Components
  • EvpB family type VI secretion proteinType VI secretion system
  • Type VI secretion protein, familyType VI secretion system
KeywordsSTRUCTURAL PROTEIN / type six secretion system / structural protein
Function / homologyType VI secretion system, VipA, VC_A0107 or Hcp2 / Type VI secretion protein, EvpB/VC_A0108, tail sheath / Type VI secretion system, VipA, VC_A0107 or Hcp2 / Type VI secretion protein, EvpB/VC_A0108, tail sheath / Type VI secretion protein, family / EvpB family type VI secretion protein / Uncharacterized protein / Uncharacterized protein
Function and homology information
Specimen sourcePseudomonas aeruginosa (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / 3.28 Å resolution
AuthorsSalih, O. / He, S. / Stach, L. / Macdonald, J.T. / Planamente, S. / Manoli, E. / Scheres, S. / Filloux, A. / Freemont, P.S.
CitationJournal: Structure / Year: 2018
Title: Atomic Structure of Type VI Contractile Sheath from Pseudomonas aeruginosa.
Authors: Osman Salih / Shaoda He / Sara Planamente / Lasse Stach / James T MacDonald / Eleni Manoli / Sjors H W Scheres / Alain Filloux / Paul S Freemont
Abstract: Pseudomonas aeruginosa has three type VI secretion systems (T6SSs), H1-, H2-, and H3-T6SS, each belonging to a distinct group. The two T6SS components, TssB/VipA and TssC/VipB, assemble to form ...Pseudomonas aeruginosa has three type VI secretion systems (T6SSs), H1-, H2-, and H3-T6SS, each belonging to a distinct group. The two T6SS components, TssB/VipA and TssC/VipB, assemble to form tubules that conserve structural/functional homology with tail sheaths of contractile bacteriophages and pyocins. Here, we used cryoelectron microscopy to solve the structure of the H1-T6SS P. aeruginosa TssB1C1 sheath at 3.3 Å resolution. Our structure allowed us to resolve some features of the T6SS sheath that were not resolved in the Vibrio cholerae VipAB and Francisella tularensis IglAB structures. Comparison with sheath structures from other contractile machines, including T4 phage and R-type pyocins, provides a better understanding of how these systems have conserved similar functions/mechanisms despite evolution. We used the P. aeruginosa R2 pyocin as a structural template to build an atomic model of the TssB1C1 sheath in its extended conformation, allowing us to propose a coiled-spring-like mechanism for T6SS sheath contraction.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 23, 2017 / Release: Jan 10, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 10, 2018Structure modelrepositoryInitial release
1.1Jan 17, 2018Structure modelDatabase referencescitation / citation_author_citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
1.2Feb 14, 2018Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)995,33830
Polyers995,33830
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)201830
ΔGint (kcal/M)-1170
Surface area (Å2)378640
MethodPISA

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Components

#1: Protein/peptide
Type VI secretion protein, family / Type VI secretion system


Mass: 14634.741 Da / Num. of mol.: 15 / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: AO964_32215, PAERUG_E15_London_28_01_14_04448, PAERUG_P32_London_17_VIM_2_10_11_02574, PAMH19_0082
Production host: Escherichia coli (E. coli) / References: UniProt: A0A072ZG09, UniProt: Q9I749*PLUS
#2: Protein/peptide
EvpB family type VI secretion protein / Type VI secretion system


Mass: 51721.125 Da / Num. of mol.: 15 / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: U769_00445 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E1AL03, UniProt: Q9I748*PLUS

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / Reconstruction method: helical reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1contracted sheath of a Pseudomonas aeruginosa T6SS consisting of TssB1 and TssC1COMPLEX1, 20RECOMBINANT
2AO964_32215, PAERUG_E15_London_28_01_14_04448, PAERUG_P32_London_17_VIM_2_10_11_02574, PAMH19_0082COMPLEX11RECOMBINANT
3U769_00445COMPLEX21RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
12287Pseudomonas aeruginosa (bacteria)
23287Pseudomonas aeruginosa (bacteria)
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganism
12562Escherichia coli (E. coli)
23562Escherichia coli (E. coli)
Buffer solutionpH: 9
SpecimenConc.: 1 mg/ml / Embedding 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
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 30 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 27.7 deg. / Axial rise/subunit: 20.2 Å / Axial symmetry: C1
3D reconstructionResolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 71264 / Symmetry type: HELICAL

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