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- PDB-9r8g: Pseudomonas putida Pore-Forming Toxin Tke5 in complex with its co... -

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Basic information

Entry
Database: PDB / ID: 9r8g
TitlePseudomonas putida Pore-Forming Toxin Tke5 in complex with its cognate Type VI adaptor protein Tap3
Components
  • DUF4123 domain-containing protein
  • Toxin VasX N-terminal region domain-containing protein
KeywordsTOXIN / Pseudomonas putida T6SS effector / Pore-Forming Toxin / MIX family domain / adaptor protein
Function / homologyDomain of unknown function DUF4123 / : / Domain of unknown function (DUF4123) / Toxin VasX, N-terminal region / VasX toxin N-terminal region / membrane / DUF4123 domain-containing protein / Toxin VasX N-terminal region domain-containing protein
Function and homology information
Biological speciesPseudomonas putida KT2440 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.77 Å
AuthorsVelazquez, C. / Zabala-Zearreta, M. / Altuna-Alvarez, J. / Albesa-Jove, D.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2021-127816NB-I00 Spain
CitationJournal: Embo J. / Year: 2025
Title: Structural insights into the antibacterial function of the Pseudomonas putida effector Tke5
Authors: Velazquez, C. / Zabala-Zearreta, M. / Paredes, C. / Civantos, C. / Altuna-Alvarez, J. / Bernal, P. / Albesa-Jove, D.
History
DepositionMay 16, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 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

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Assembly

Deposited unit
A: Toxin VasX N-terminal region domain-containing protein
B: DUF4123 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)145,6142
Polymers145,6142
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 VasX N-terminal region domain-containing protein


Mass: 109903.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida KT2440 (bacteria) / Gene: PP_2612 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q88JN7
#2: Protein DUF4123 domain-containing protein


Mass: 35710.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida KT2440 (bacteria) / Gene: PP_2613 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q88JN6
Has protein modificationN

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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: Pseudomonas putida Pore-Forming Toxin Tke5 in complex with its cognate Type VI adaptor protein Tap3
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.145 MDa / Experimental value: NO
Source (natural)Organism: Pseudomonas putida KT2440 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMSodium chlorideNaCl1
220 mMTris (hydroxymethyl) aminomethane (THAM) hydrochlorideTris-HCl1
32 mMDithiothreitolDTT1
40.05 %w/v3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonateCHAPS1
SpecimenConc.: 2.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / 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: 2500 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 48.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
2PHENIX1.21.2_5419model refinement
3EPUimage acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 381732 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 104.61 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00359026
ELECTRON MICROSCOPYf_angle_d0.451612361
ELECTRON MICROSCOPYf_chiral_restr0.03871420
ELECTRON MICROSCOPYf_plane_restr0.00371618
ELECTRON MICROSCOPYf_dihedral_angle_d9.97963059

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