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- PDB-6riu: C-terminal domain of TssA protein from T6SS of Vibrio cholerae. -

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Basic information

Entry
Database: PDB / ID: 6riu
TitleC-terminal domain of TssA protein from T6SS of Vibrio cholerae.
ComponentsType VI secretion system protein TssAType VI secretion system
KeywordsTRANSPORT PROTEIN / T6SS / Vibrio / TssA / cap
Function / homologyType VI secretion system-associated, VCA0119 / Type VI secretion, EvfE, EvfF, ImpA, BimE, VC_A0119, VasJ / ImpA, N-terminal / ImpA, N-terminal, type VI secretion system / Type VI secretion system protein TssA / ImpA_N domain-containing protein
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsNazarov, S. / Basler, M.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science FoundationBSSGI0_155778 Switzerland
CitationJournal: EMBO J / Year: 2019
Title: Diverse roles of TssA-like proteins in the assembly of bacterial type VI secretion systems.
Authors: Johannes Paul Schneider / Sergey Nazarov / Ricardo Adaixo / Martina Liuzzo / Peter David Ringel / Henning Stahlberg / Marek Basler /
Abstract: Protein translocation by the bacterial type VI secretion system (T6SS) is driven by a rapid contraction of a sheath assembled around a tube with associated effectors. Here, we show that TssA-like or ...Protein translocation by the bacterial type VI secretion system (T6SS) is driven by a rapid contraction of a sheath assembled around a tube with associated effectors. Here, we show that TssA-like or TagA-like proteins with a conserved N-terminal domain and varying C-terminal domains can be grouped into at least three distinct classes based on their role in sheath assembly. The proteins of the first class increase speed and frequency of sheath assembly and form a stable dodecamer at the distal end of a polymerizing sheath. The proteins of the second class localize to the cell membrane and block sheath polymerization upon extension across the cell. This prevents excessive sheath polymerization and bending, which may result in sheath destabilization and detachment from its membrane anchor and thus result in failed secretion. The third class of these proteins localizes to the baseplate and is required for initiation of sheath assembly. Our work shows that while various proteins share a conserved N-terminal domain, their roles in T6SS biogenesis are fundamentally different.
History
DepositionApr 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.journal_volume / _entity_src_gen.pdbx_gene_src_gene ..._citation.journal_volume / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession

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Structure visualization

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Assembly

Deposited unit
A: Type VI secretion system protein TssA
B: Type VI secretion system protein TssA


Theoretical massNumber of molelcules
Total (without water)106,2062
Polymers106,2062
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1380 Å2
ΔGint-11 kcal/mol
Surface area11040 Å2
MethodPISA

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Components

#1: Protein Type VI secretion system protein TssA / Type VI secretion system


Mass: 53102.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: tssA, EEJ33_15620, EEJ37_01920 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A023PTF2, UniProt: Q9KN46*PLUS

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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

Component
IDNameTypeEntity IDParent-IDSource
1Type VI secretion system protein TssA.Type VI secretion systemCOMPLEXall0NATURAL
2Middle N-terminal domain (Nt2) of TssA protein from T6SS of Vibrio cholerae.COMPLEXall1NATURAL
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.634 MDaYES
12
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Vibrio cholerae (bacteria)666
32Vibrio cholerae (bacteria)666
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in.
VitrificationCryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 293 K / Details: Leica EM GP2

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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 FIELDBright-field microscopy / Cs: 2.7 mm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 2963
EM imaging opticsEnergyfilter name: GIF Quantum LS
Image scansMovie frames/image: 40

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Processing

EM software
IDNameCategory
1Gautomatchparticle selection
2SerialEMimage acquisition
4CTFFINDCTF correction
9PHENIXmodel refinement
11RELIONfinal Euler assignment
13RELION3D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 261412
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31781 / Symmetry type: POINT
Atomic model buildingPDB-ID: 6G7C

6g7c


Pdb chain-ID: A / Pdb chain residue range: 388-474

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