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- EMDB-53284: Pseudomonas aeruginosa Ptx2 toxin -

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Basic information

Entry
Database: EMDB / ID: EMD-53284
TitlePseudomonas aeruginosa Ptx2 toxin
Map dataLocal resolution-filtered map used for model building
Sample
  • Organelle or cellular component: Ptx2 toxin
    • Protein or peptide: Ptx2 toxin
Keywordstoxin / soluble protein / pre-pore state
Function / homologyToxin VasX, N-terminal region / VasX toxin N-terminal region / Toxin VasX N-terminal region domain-containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsShatskiy D / Belyy A
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Rep / Year: 2025
Title: Cryo-EM structure of a type VI secretion system-delivered membrane-depolarizing toxin involved in bacterial antagonism.
Authors: Jake Colautti / Dmitry Shatskiy / Eileen M Bates / Nathan P Bullen / Alexander Belyy / John C Whitney /
Abstract: Many Gram-negative bacteria use type VI secretion systems (T6SSs) to deliver toxic effector proteins into neighboring cells. Proteins in the VasX toxin family form ion-permeable channels in the ...Many Gram-negative bacteria use type VI secretion systems (T6SSs) to deliver toxic effector proteins into neighboring cells. Proteins in the VasX toxin family form ion-permeable channels in the bacterial cytoplasmic membrane that dissipate the proton motive force, thereby interfering with essential physiological processes. However, the structure of any VasX family effector has remained unknown. Here, we present a cryo-EM structure of Ptx2, a recently identified VasX family effector exported by a T6SS of Pseudomonas aeruginosa. Our structure reveals that Ptx2 is an elongated, multi-domain protein that bears little resemblance to proteins of known function. Notably, the apparent flexibility of its domains suggests that Ptx2 undergoes substantial conformational changes to facilitate membrane insertion. Guided by these predicted structural rearrangements, we used mutagenesis coupled with phenotypic assays to identify key features required for its toxic activity. Together, these findings provide molecular insights into the structure and mechanism of VasX family effectors.
History
DepositionMar 29, 2025-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53284.png

Downloads & links

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Map

FileDownload / File: emd_53284.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal resolution-filtered map used for model building
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 256 pix.
= 215.04 Å		0.84 Å/pix.
x 256 pix.
= 215.04 Å		0.84 Å/pix.
x 256 pix.
= 215.04 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0025
Minimum - Maximum-0.014083422 - 0.02774072
Average (Standard dev.)-0.000015797348 (±0.000648004)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 215.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_53284_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_53284_half_map_2.map
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Sample components

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Entire : Ptx2 toxin

EntireName: Ptx2 toxin
Components
  • Organelle or cellular component: Ptx2 toxin
    • Protein or peptide: Ptx2 toxin

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Supramolecule #1: Ptx2 toxin

SupramoleculeName: Ptx2 toxin / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)

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Macromolecule #1: Ptx2 toxin

MacromoleculeName: Ptx2 toxin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 131.467609 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SQDPNSSSMT AQATPRRDSA NLAANEASSS DSRSPSGTCP LMNAKVQLLP LRYGLTEGVD PSAELAMPFA LKSRPLGLR LVRNGYLYVI DGGTGKLHEY RIDKGAIDKL LWQDAEVRAD VRSRAVGEPQ LVFPRTSVLY VAYSELQWTA R KCMQVLAS ...String:
MGSSHHHHHH SQDPNSSSMT AQATPRRDSA NLAANEASSS DSRSPSGTCP LMNAKVQLLP LRYGLTEGVD PSAELAMPFA LKSRPLGLR LVRNGYLYVI DGGTGKLHEY RIDKGAIDKL LWQDAEVRAD VRSRAVGEPQ LVFPRTSVLY VAYSELQWTA R KCMQVLAS PKDREHFMQA VDLRRADPQQ GGPHLLTRRQ AETWLAEVVQ NKVHRDEQGQ QRFPPHQQRP ASPPAAHPDE RR DYVWEDP PLFRDTQLGE LTAQVLPQYE HDALFLALRD DIGVMRDLAA YQDEVVGWLE EWLQGGAQAG ANERDYVIAC YIE SLTQIR AAELPKLADE SAQPLFDDLD RLPPPERERS RQALLDYLNG EPLPKPMDPA MPEPLHRPVE RHFTKRKMAV ADPA FVERN LDALIRLKKS HGEKVDDALH GAKFGQRGID DLIDRPAMDS FLAANRPNLA RWNALLEQIS ADRTQMLTEQ RFHRA AWYY DFQQAEQLGL AFATQYACLK DICRSDEASE AVLAFLEENP QYDRPLFQTL PLNTQAELIA QYAQLGPPGH LWLSKL KEW AQQRDSLELG KLPALDGLPE ATRALADSAQ ATLNPALTLG ISRTMEGFFK SVGQQQAPDL DALFRKLPKA LPGRLLD AA VREGVTFTIA SEAEKAILQA DLKEVLEQRA ELRRLVRQRK QVKSQAGHKS TDARALLADI QRVRLQLNAL EPRLAAAL S PIAELPDNSI RLAGATPGRA GITLILPSAQ LQEVASGIRN LRNGYSSAAA FNKVGDGIGL AVFVAQFVNM VQVWRGVIA TSPDKRELMP LAGSIFTTIS AGVAAAQAIA DTALQARSVQ LAQGLQNHAV EVAHVQMGKL HLRLGFVGYA AGFFAAAVAT QTHYGEWLG AIRSGNAQAQ QGAALAMVGS SGMLASSAYG VWHTGYALKG VLRAATPAAE RTAWALAGTR LSSIFARFNI A GAIFTALE LVGTYWYNRS NTTPHDDWLL STPWSRDIGG RLNQSLEIYQ QRLLGIVQTP RGEVKHASHG SWWRDLLSSS AT AEISLAL PGISLGALQQ TLAGRPEVRL SLAAYRIRSV KYERGSPMVR WFPVTEVVGD SLQVASAEPL VLLVPRLAPL EGV TGGSVT EDLLLAVQIE RLNPQGQYHA DRHMVRLSPH SEGDYPASPQ RIQGQEASWM LIDPRLLPDF ADAPER

UniProtKB: Toxin VasX N-terminal region domain-containing protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 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: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 684417
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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