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- EMDB-53274: Hcp3-Tce1 complex from the Pseudomonas aeruginosa Type VI Secreti... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-53274
TitleHcp3-Tce1 complex from the Pseudomonas aeruginosa Type VI Secretion System
Map data
Sample
  • Complex: Tce1 toxin in complex with the Hcp3 hexameric ring
    • Protein or peptide: Hcp family type VI secretion system effector
    • Protein or peptide: DUF4347 domain-containing protein
KeywordsT6SS / cysteine protease / effector / Hcp / Hcp3 / Tce1 / PROTEIN TRANSPORT
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsParacuellos P / Bexter A / Patkowski JB / Omelchenko O / Mace K / Ilangovan A / Filloux A / Costa TRD
Funding support United Kingdom, 1 items
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 JB / Omelchenko O / Mace K / Ilangovan A / Filloux A / Costa TRD
History
DepositionMar 27, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53274.png

Downloads & links

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Map

FileDownload / File: emd_53274.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 320 pix.
= 294.72 Å		0.92 Å/pix.
x 320 pix.
= 294.72 Å		0.92 Å/pix.
x 320 pix.
= 294.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.921 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.55
Minimum - Maximum-7.197381 - 7.621149
Average (Standard dev.)-0.0015902172 (±0.082287185)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 294.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_53274_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_53274_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Tce1 toxin in complex with the Hcp3 hexameric ring

EntireName: Tce1 toxin in complex with the Hcp3 hexameric ring
Components
  • Complex: Tce1 toxin in complex with the Hcp3 hexameric ring
    • Protein or peptide: Hcp family type VI secretion system effector
    • Protein or peptide: DUF4347 domain-containing protein

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Supramolecule #1: Tce1 toxin in complex with the Hcp3 hexameric ring

SupramoleculeName: Tce1 toxin in complex with the Hcp3 hexameric ring / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 139.1 KDa

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Macromolecule #1: Hcp family type VI secretion system effector

MacromoleculeName: Hcp family type VI secretion system effector / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 17.650811 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MDAIILDFGS DIKGDSLLVG YENKIEIMSY SHNVAMQVTN DVSNSERTSG KPHVGEFTLT KFIDTSTPTL NEYCCAGKPI AEATITIGR NAAEGNGQIM PFIVYTLNNV VLSNVSVSGG AGGKPVETLS LNFTKIKWEL TAQKDDGTKE GTAASTWDLA A NQLVK

UniProtKB: Hcp family type VI secretion system effector

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Macromolecule #2: DUF4347 domain-containing protein

MacromoleculeName: DUF4347 domain-containing protein / type: protein_or_peptide / ID: 2 / Details: Tce1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 21.622418 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: KGAVLVIYHD FQQEIRRGDS GSAFAEAVVA YARNKLYKPA FAIKADTNYA QLVRDLGKVA AESGEQYFID TILIATHGTA GQLWLGNPH GDSTADVMAR RVQGKQFVEP QAFGATLLEL FGKELAIALY GCDFAGDEDG EAAALELRIA ANARAVYAGK G TVYLNASK ...String:
KGAVLVIYHD FQQEIRRGDS GSAFAEAVVA YARNKLYKPA FAIKADTNYA QLVRDLGKVA AESGEQYFID TILIATHGTA GQLWLGNPH GDSTADVMAR RVQGKQFVEP QAFGATLLEL FGKELAIALY GCDFAGDEDG EAAALELRIA ANARAVYAGK G TVYLNASK EGRSTVTCSK AMVVYRTDKI EVLGGNQVPV FDI

UniProtKB: DUF4347 domain-containing protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 166948
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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