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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 protein
  • Type VI secretion protein, family
KeywordsSTRUCTURAL PROTEIN / type six secretion system
Function / homology
Function and homology information


Type VI secretion system TssC-like / TssC1, N-terminal / TssC1, C-terminal / EvpB/VC_A0108, tail sheath N-terminal domain / EvpB/VC_A0108, tail sheath gpW/gp25-like domain / Type VI secretion system sheath protein TssB1 / Type VI secretion system, VipA, VC_A0107 or Hcp2
Similarity search - Domain/homology
Type VI secretion system contractile sheath small subunit / : / Type VI secretion system sheath protein TssC1 / Type VI secretion system sheath protein TssB1
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.28 Å
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.
History
DepositionFeb 23, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Feb 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3May 15, 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: 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
Polymers995,33830
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area201830 Å2
ΔGint-1170 kcal/mol
Surface area378640 Å2
MethodPISA

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Components

#1: Protein
Type VI secretion protein, family


Mass: 14634.741 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
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
EvpB family type VI secretion protein


Mass: 51721.125 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
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 / 3D 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 TssC1COMPLEXall0RECOMBINANT
2AO964_32215, PAERUG_E15_London_28_01_14_04448, PAERUG_P32_London_17_VIM_2_10_11_02574, PAMH19_0082COMPLEX#11RECOMBINANT
3U769_00445COMPLEX#21RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Pseudomonas aeruginosa (bacteria)287
23Pseudomonas aeruginosa (bacteria)287
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Escherichia coli (E. coli)562
23Escherichia coli (E. coli)562
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
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
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 ° / Axial rise/subunit: 20.2 Å / Axial symmetry: C1
3D reconstructionResolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 71264 / Symmetry type: HELICAL

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