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- EMDB-52772: Visualization of the full-length Tse5-CT toxic fragment inside T6... -

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Basic information

Entry
Database: EMDB / ID: EMD-52772
TitleVisualization of the full-length Tse5-CT toxic fragment inside T6SS-dependent Tse5 effector
Map data
Sample
  • Complex: Visualization of the full-length Tse5-CT toxic fragment inside T6SS-dependent Tse5 effector
    • Protein or peptide: Toxin protein Tse5
    • Protein or peptide: Toxin protein Tse5
    • Protein or peptide: Toxin protein Tse5
KeywordsToxin / Type VI Secretion System / Pseudomonas aeruginosa / Rearrangement hotspot (Rhs)
Function / homology
Function and homology information


protein secretion by the type VI secretion system / toxin sequestering activity
Similarity search - Function
RHS protein / RHS protein / RHS repeat / RHS Repeat / Domain of unknown function DUF6531 / Domain of unknown function (DUF6531) / YD repeat / : / Rhs repeat-associated core
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.22 Å
AuthorsAltuna-Alvarez J / Zabala-Zearreta M / Albesa-Jove D
Funding support Spain, 2 items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2021-127816NB-I00 Spain
Other governmentIT1745-22
CitationJournal: To Be Published
Title: Visualization of the full-length Tse5-CT toxic fragment inside T6SS-dependent Tse5 effector
Authors: Altuna-Alvarez J / Zabala-Zearreta M / Albesa-Jove D
History
DepositionFeb 7, 2025-
Header (metadata) releaseAug 19, 2026-
Map releaseAug 19, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52772.png

Downloads & links

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Map

FileDownload / File: emd_52772.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 400 pix.
= 258.48 Å		0.65 Å/pix.
x 400 pix.
= 258.48 Å		0.65 Å/pix.
x 400 pix.
= 258.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.6462 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0811
Minimum - Maximum-0.16011687 - 0.42778003
Average (Standard dev.)0.00014434746 (±0.010354299)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 258.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52772_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52772_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52772_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Visualization of the full-length Tse5-CT toxic fragment inside T6...

EntireName: Visualization of the full-length Tse5-CT toxic fragment inside T6SS-dependent Tse5 effector
Components
  • Complex: Visualization of the full-length Tse5-CT toxic fragment inside T6SS-dependent Tse5 effector
    • Protein or peptide: Toxin protein Tse5
    • Protein or peptide: Toxin protein Tse5
    • Protein or peptide: Toxin protein Tse5

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Supramolecule #1: Visualization of the full-length Tse5-CT toxic fragment inside T6...

SupramoleculeName: Visualization of the full-length Tse5-CT toxic fragment inside T6SS-dependent Tse5 effector
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PA01
Molecular weightTheoretical: 148.77586 KDa

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Macromolecule #1: Toxin protein Tse5

MacromoleculeName: Toxin protein Tse5 / type: protein_or_peptide / ID: 1
Details: The protein is synthesized as a single pro-peptide, but undergoes autoproteolytic maturation, during which it is proteolyzed into three fragments. These three fragments remain mostly linked ...Details: The protein is synthesized as a single pro-peptide, but undergoes autoproteolytic maturation, during which it is proteolyzed into three fragments. These three fragments remain mostly linked by noncovalent bonds. This fragment belongs to the N-terminal fragment (residues 1-47).
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 7.456322 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
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
Details: The protein is synthesized as a single pro-peptide, but undergoes autoproteolytic maturation, during which it is proteolyzed into three fragments. These three fragments remain mostly linked ...Details: The protein is synthesized as a single pro-peptide, but undergoes autoproteolytic maturation, during which it is proteolyzed into three fragments. These three fragments remain mostly linked by noncovalent bonds. This fragment belongs to the central fragment (residues 48-1168).
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 125.970461 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
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
Details: The protein is synthesized as a single pro-peptide, but undergoes autoproteolytic maturation, during which it is proteolyzed into three fragments. These three fragments remain mostly linked ...Details: The protein is synthesized as a single pro-peptide, but undergoes autoproteolytic maturation, during which it is proteolyzed into three fragments. These three fragments remain mostly linked by noncovalent bonds. This fragment belongs to the C-terminal fragment (residues 1169-1317).
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (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

Concentration3 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloride
20.0 mMTrisTris(hydroxymethyl)aminomethane
2.0 mMDTTDithiothreitol
0.05 %CHAPS3-[(3-cholamidopropyl)dimethylammonio]propane-1-sulfonate
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 5 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 180 sec. / Pretreatment - Pressure: 41.0 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 47.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.826 µm / Nominal defocus min: 0.8 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: PDB ENTRY
PDB model - PDB ID:

8cp6

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.22 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 749052
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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