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- PDB-9i9y: Visualization of the full-length Tse5-CT toxic fragment inside T6... -

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Basic information

Entry
Database: PDB / ID: 9i9y
TitleVisualization of the full-length Tse5-CT toxic fragment inside T6SS-dependent Tse5 effector
Components(Toxin protein Tse5) x 3
KeywordsTOXIN / Type VI Secretion System / Pseudomonas aeruginosa / Rearrangement hotspot (Rhs)
Function / homology
Function and homology information


protein secretion by the type VI secretion system / toxin sequestering activity
Similarity search - Function
RHS protein / RHS protein / RHS repeat / RHS Repeat / Domain of unknown function DUF6531 / Domain of unknown function (DUF6531) / YD repeat / : / Rhs repeat-associated core
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.22 Å
AuthorsAltuna-Alvarez, J. / Zabala-Zearreta, M. / Albesa-Jove, D.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2021-127816NB-I00 Spain
Other governmentIT1745-22
CitationJournal: To Be Published
Title: Visualization of the full-length Tse5-CT toxic fragment inside T6SS-dependent Tse5 effector
Authors: Altuna-Alvarez, J. / Zabala-Zearreta, M. / Albesa-Jove, D.
History
DepositionFeb 7, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Toxin protein Tse5
B: Toxin protein Tse5
C: Toxin protein Tse5


Theoretical massNumber of molelcules
Total (without water)149,0193
Polymers149,0193
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Toxin protein Tse5


Mass: 7456.322 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The protein is synthesized as a single pro-peptide, but undergoes autoproteolytic maturation, during which it is proteolyzed into three fragments. These three fragments remain mostly linked ...Details: The protein is synthesized as a single pro-peptide, but undergoes autoproteolytic maturation, during which it is proteolyzed into three fragments. These three fragments remain mostly linked by noncovalent bonds. This fragment belongs to the N-terminal fragment (residues 1-47).
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: tse5, PA2684 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9I0F4
#2: Protein Toxin protein Tse5


Mass: 125970.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The protein is synthesized as a single pro-peptide, but undergoes autoproteolytic maturation, during which it is proteolyzed into three fragments. These three fragments remain mostly linked ...Details: The protein is synthesized as a single pro-peptide, but undergoes autoproteolytic maturation, during which it is proteolyzed into three fragments. These three fragments remain mostly linked by noncovalent bonds. This fragment belongs to the central fragment (residues 48-1168).
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: tse5, PA2684 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9I0F4
#3: Protein Toxin protein Tse5


Mass: 15592.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The protein is synthesized as a single pro-peptide, but undergoes autoproteolytic maturation, during which it is proteolyzed into three fragments. These three fragments remain mostly linked ...Details: The protein is synthesized as a single pro-peptide, but undergoes autoproteolytic maturation, during which it is proteolyzed into three fragments. These three fragments remain mostly linked by noncovalent bonds. This fragment belongs to the C-terminal fragment (residues 1169-1317).
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: tse5, PA2684 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I0F4
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: Visualization of the full-length Tse5-CT toxic fragment inside T6SS-dependent Tse5 effector
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.14877586 MDa / Experimental value: NO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PA01
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: BL21
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMSodium chlorideNaCl1
220 mMTris(hydroxymethyl)aminomethaneTris1
32 mMDithiothreitolDTT1
40.05 %3-[(3-cholamidopropyl)dimethylammonio]propane-1-sulfonateCHAPS1
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2826 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 47.7 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5.3particle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC4.5.33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 749052 / Symmetry type: POINT
RefinementHighest resolution: 2.22 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039842
ELECTRON MICROSCOPYf_angle_d0.52513328
ELECTRON MICROSCOPYf_dihedral_angle_d4.0071417
ELECTRON MICROSCOPYf_chiral_restr0.0421363
ELECTRON MICROSCOPYf_plane_restr0.0041801

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