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- PDB-9qpe: Hcp3-Tce1 complex from the Pseudomonas aeruginosa Type VI Secreti... -

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Basic information

Entry
Database: PDB / ID: 9qpe
TitleHcp3-Tce1 complex from the Pseudomonas aeruginosa Type VI Secretion System
Components
  • DUF4347 domain-containing protein
  • Hcp family type VI secretion system effector
KeywordsPROTEIN TRANSPORT / T6SS / cysteine protease / effector / Hcp / Hcp3 / Tce1
Function / homology: / Type VI secretion system effector Hcp / Hcp1-like superfamily / Type VI secretion system effector, Hcp / Hcp family type VI secretion system effector / DUF4347 domain-containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsParacuellos, P. / Bexter, A. / Patkowski, J.B. / Omelchenko, O. / Mace, K. / Ilangovan, A. / Filloux, A. / Costa, T.R.D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Imperial College London United Kingdom
CitationJournal: To Be Published
Title: Molecular basis for toxin delivery by a Type VI Secretion System
Authors: Paracuellos, P. / Bexter, A. / Patkowski, J.B. / Omelchenko, O. / Mace, K. / Ilangovan, A. / Filloux, A. / Costa, T.R.D.
History
DepositionMar 27, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Hcp family type VI secretion system effector
B: Hcp family type VI secretion system effector
C: Hcp family type VI secretion system effector
D: Hcp family type VI secretion system effector
E: Hcp family type VI secretion system effector
F: Hcp family type VI secretion system effector
G: DUF4347 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)127,5277
Polymers127,5277
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
Hcp family type VI secretion system effector / Type VI secretion effector protein (Hcp) / Type VI secretion system tube protein Hcp


Mass: 17650.811 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: CAZ10_33725, GNQ48_24960, GUL26_29960, IPC1295_17020, L4V69_18200, PAERUG_P19_London_7_VIM_2_05_10_04092
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A069PXC4
#2: Protein DUF4347 domain-containing protein / Tce1


Mass: 21622.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Tce1 / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA0256 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9I6N3
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Tce1 toxin in complex with the Hcp3 hexameric ring / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.1391 MDa / Experimental value: NO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding 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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2700 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 166948 / Symmetry type: POINT

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