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- PDB-6rju: C-terminal domain of TssA protein from T6SS of Escherichia coli. -

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Basic information

Entry
Database: PDB / ID: 6rju
TitleC-terminal domain of TssA protein from T6SS of Escherichia coli.
ComponentsPutative type VI secretion protein
KeywordsTRANSPORT PROTEIN / T6SS / E. coli / 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 / Putative type VI secretion protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsNazarov, S. / Shneider, M. / Basler, M. / Leiman, P.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science FoundationBSSGI0_155778 Switzerland
CitationJournal: To Be Published
Title: Cryo-EM structure of TssA protein from Type VI secretion system of E. coli.
Authors: Nazarov, S. / Demurtas, D. / Shneider, M. / Basler, M. / Leiman, P.
History
DepositionApr 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
A: Putative type VI secretion protein


Theoretical massNumber of molelcules
Total (without water)59,1601
Polymers59,1601
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9690 Å2
MethodPISA

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Components

#1: Protein Putative type VI secretion protein


Mass: 59159.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: NCTC12950_00920 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A376XSV1
Has protein modificationY

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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: C-terminal domain of T6SS protein TssA. / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.634 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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 FIELD / 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: 3269
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
7Situsmodel fitting
10RELIONfinal Euler assignment
11RELIONclassification
12RELION3D reconstruction
13PHENIXmodel refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 667861
SymmetryPoint symmetry: D6 (2x6 fold dihedral)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 52370 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingPDB-ID: 4YO5

4yo5


Pdb chain-ID: A / Accession code: 4YO5 / Pdb chain residue range: 388-474 / Source name: PDB / Type: experimental model

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