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- EMDB-16778: Type six secretion system exported effector 5 (Tse5) -

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Basic information

Entry
Database: EMDB / ID: EMD-16778
TitleType six secretion system exported effector 5 (Tse5)
Map data
Sample
  • Organelle or cellular component: Tse5
    • Protein or peptide: Toxin protein Tse5
    • Protein or peptide: Toxin protein Tse5
    • Protein or peptide: Toxin protein Tse5
KeywordsPore-forming protein / P.aeruginosa / effector / Bacterial Rearrangement hot spot protein / ion channel / type VI secretion system / TOXIN
Function / homology
Function and homology information


protein secretion by the type VI secretion system / toxin sequestering activity
Similarity search - Function
Domain of unknown function DUF6531 / RHS protein / Domain of unknown function (DUF6531) / RHS protein / RHS repeat / RHS Repeat / YD repeat / Rhs repeat-associated core / :
Similarity search - Domain/homology
Biological speciesPseudomonas (RNA similarity group I) / Pseudomonas aeruginosa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.45 Å
AuthorsGonzalez-Magana A / Tascon I / Ubarretxena-Belandia I / Albesa-Jove D
Funding support Spain, 2 items
OrganizationGrant numberCountry
Other governmentIT1745-22
Spanish Ministry of Science, Innovation, and UniversitiesPID2021-127816NB-I00 Spain
CitationJournal: Nat Commun / Year: 2023
Title: Structural and functional insights into the delivery of a bacterial Rhs pore-forming toxin to the membrane.
Authors: Amaia González-Magaña / Igor Tascón / Jon Altuna-Alvarez / María Queralt-Martín / Jake Colautti / Carmen Velázquez / Maialen Zabala / Jessica Rojas-Palomino / Marité Cárdenas / ...Authors: Amaia González-Magaña / Igor Tascón / Jon Altuna-Alvarez / María Queralt-Martín / Jake Colautti / Carmen Velázquez / Maialen Zabala / Jessica Rojas-Palomino / Marité Cárdenas / Antonio Alcaraz / John C Whitney / Iban Ubarretxena-Belandia / David Albesa-Jové /
Abstract: Bacterial competition is a significant driver of toxin polymorphism, which allows continual compensatory evolution between toxins and the resistance developed to overcome their activity. Bacterial ...Bacterial competition is a significant driver of toxin polymorphism, which allows continual compensatory evolution between toxins and the resistance developed to overcome their activity. Bacterial Rearrangement hot spot (Rhs) proteins represent a widespread example of toxin polymorphism. Here, we present the 2.45 Å cryo-electron microscopy structure of Tse5, an Rhs protein central to Pseudomonas aeruginosa type VI secretion system-mediated bacterial competition. This structural insight, coupled with an extensive array of biophysical and genetic investigations, unravels the multifaceted functional mechanisms of Tse5. The data suggest that interfacial Tse5-membrane binding delivers its encapsulated pore-forming toxin fragment to the target bacterial membrane, where it assembles pores that cause cell depolarisation and, ultimately, bacterial death.
History
DepositionMar 1, 2023-
Header (metadata) releaseDec 6, 2023-
Map releaseDec 6, 2023-
UpdateDec 6, 2023-
Current statusDec 6, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16778.png

Downloads & links

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Map

FileDownload / File: emd_16778.map.gz / Format: CCP4 / Size: 52.7 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 240 pix.
= 221.04 Å		0.92 Å/pix.
x 240 pix.
= 221.04 Å		0.92 Å/pix.
x 240 pix.
= 221.04 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: 0.177
Minimum - Maximum-0.34572968 - 0.808894
Average (Standard dev.)0.00196805 (±0.023979845)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 221.04001 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16778_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_16778_half_map_1.map
Projections & Slices
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Histogram

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Half map: #1

Fileemd_16778_half_map_2.map
Projections & Slices
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Sample components

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Entire : Tse5

EntireName: Tse5
Components
  • Organelle or cellular component: Tse5
    • Protein or peptide: Toxin protein Tse5
    • Protein or peptide: Toxin protein Tse5
    • Protein or peptide: Toxin protein Tse5

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Supramolecule #1: Tse5

SupramoleculeName: Tse5 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Pseudomonas aeruginosa type VI secretion system (T6SS) exported effector Tse5. The three chains result from the auto-cleavage of Tse5
Source (natural)Organism: Pseudomonas (RNA similarity group I)
Molecular weightTheoretical: 146 KDa

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Macromolecule #1: Toxin protein Tse5

MacromoleculeName: Toxin protein Tse5 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 7.456322 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MMGSSHHHHH HHHHSSGENL YFQGGSMSGL PVSHVGEKVS GGVISTGSPT VHVGSSAVGL ADRVSACVPL VGK

UniProtKB: Toxin protein Tse5

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Macromolecule #2: Toxin protein Tse5

MacromoleculeName: Toxin protein Tse5 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 125.970461 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: PVNPMLGSKL LPEEVDFALA APDTFTFARG YLSSNPRIGR LGRGWWLPGE SMHLELSEDA CVLVDAQGRR IGFPALAPGA QHYSGSEEL WLRRGGSSGG EAQAWRGRWA AVPAELQTQE GSVLVLSGHS YLHFQRCPDG IWRLQASFGR AGYRTEFRWS G RGLLTGVR ...String:
PVNPMLGSKL LPEEVDFALA APDTFTFARG YLSSNPRIGR LGRGWWLPGE SMHLELSEDA CVLVDAQGRR IGFPALAPGA QHYSGSEEL WLRRGGSSGG EAQAWRGRWA AVPAELQTQE GSVLVLSGHS YLHFQRCPDG IWRLQASFGR AGYRTEFRWS G RGLLTGVR DSAGRSYALV YQQACEPSEG DDGLRLFGVI LASHDGPPPD YIDPQSPGLD WLVRYQFSDS GDLIAVRDRL GQ VVRVFAW REHMLVAHGE PGGLEVRYEW DVHAPHGRVV KQIEAGGLTR TFRYLRDATE VSDSLGRVER YEFAGEGGQR RWT ALVRAD GSRSEFDYDL FGRLVAMRDP LGRETRRRRD GQGRMLEEES PGKARYRKRV DEETGLLVEL EDAMQRRWTF ERDE RGNAT TVRGPAGSTR YAYEDPRLPD RPTRIVDPRG GERRLEWNRF GLLAALTDCS GQVWRYDYDN EGRLVASSDP LGQLT RRRY DPLGQLIGLE LADGSALSYE YDALGRQTRI ADAEGHATLF SWGHGDLLAR VSDAGGGELS YLHDEAGRLV ALTNEN GVQ AQFRYDLLDR LVEETGFDGR RQRYRYNAAD ELIAREDADG RETTYAYDRD GRLASIRVPA TEHAPALVER YRWLADG RL ASAGGADCEV RYTYDEVGNL RLESQVHADG WVYSVEHSHD ALGVRQTSRY GDAPPVAWLT YGPGHLHGAL VGAVELAF E RDALHREVRR DARRDGQDDA LFTQERQHAP LGRLQRSRLR LAGGFDWQRG YRYDGLGQLV GIDDNQYPSV RYEYDLGGR LLASRRAGAA ASTYRYDAAG NRLEGVGEHA REDARQAFAE NELYRSGFSR SETRASQAGE GPARWAGNRV ERIAGNRYRF DALGNLVER IGADGERLRL AYDGAQRLVH LTRDYADGTR LEARYRYDAL SRRIAKVVLR DGVEQQVRFG WDGDRQCAEA F ARELRTTV HEPGGFVPLL RLEQACEPDP PELLQLRQAF AAEGQPLPAQ CVPALGEARI AFFHTDHLGT PLQLSDERGQ LR WQGVPDD WRAVAPERQP GAQPIRFQGQ YHDEESGLYY NRYRYYLPEA GRYASQDPLG LGGGPNPYAY ALNAPTLAYD PTG L

UniProtKB: Toxin protein Tse5

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Macromolecule #3: Toxin protein Tse5

MacromoleculeName: Toxin protein Tse5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 15.592012 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
IIPLVVIGAF AARAAIGAAL GAGIELGMQT GKQVLGQMKD NWDSDRDLTD IKWKCIDINW KHVGASAAIG TVAPGMLSTG KTVVQSAKA IRTLSGQAAN TANRAAKLAA RKAAHADTIK KAVATQAAWQ TGKQIVKCPL KDEEEECPPQ

UniProtKB: Toxin protein Tse5

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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

Concentration5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris HCl
150.0 mMNaClNaCl
2.0 mMC4H10O2S2DTT
GridModel: Quantifoil / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 3.6 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 94 % / Chamber temperature: 289 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 10244 / Average exposure time: 10.84 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4866119
Startup modelType of model: INSILICO MODEL / In silico model: Ab initio model
Final reconstructionNumber classes used: 3 / Resolution.type: BY AUTHOR / Resolution: 2.45 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 323963
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC (ver. 4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: Buccanner
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8cp6:
Type six secretion system exported effector 5 (Tse5)

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