[English] 日本語
Yorodumi
- EMDB-16778: Type six secretion system exported effector 5 (Tse5) -

+
Open data


ID or keywords:

Loading...

-
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 / Domain of unknown function (DUF6531) / RHS protein / RHS protein / RHS repeat / RHS Repeat / YD repeat / Rhs repeat-associated core
Similarity search - Domain/homology
Biological speciesPseudomonas (bacteria) / 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

-
Structure visualization

Supplemental images

emd_16778.png

Downloads & links

-
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 °

-
Supplemental data

-
Mask #1

Fileemd_16778_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_16778_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_16778_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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 (bacteria)
Molecular weightTheoretical: 146 KDa

-
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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris HCl
150.0 mMNaClSodium chlorideNaClSodium chloride
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

-
Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 4866119
Startup modelType of model: INSILICO MODEL / In silico model: Ab initio model
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)
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
FSC plot (resolution estimation)

-
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more