[English] 日本語
Yorodumi
- EMDB-10218: Structure of the Tle1 effector bound to the VgrG spike from the T... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10218
TitleStructure of the Tle1 effector bound to the VgrG spike from the Type 6 secretion system
Map dataSharpened map
Sample
  • Complex: Tle1 effector bound to the VgrG spike of the type 6 secretion system
    • Protein or peptide: Putative type VI secretion protein
    • Protein or peptide: Putative type VI secretion protein
KeywordsHydrolase / toxin / lipase / effector / bacterial
Function / homology
Function and homology information


Domain of unknown function DUF2235 / T6SS, Phospholipase effector Tle1-like, catalytic domain / Type VI secretion system spike protein VgrG2, C-terminal domain of unknown function DUF2345 / Putative type VI secretion system, Rhs element associated Vgr domain / Uncharacterized protein conserved in bacteria (DUF2345) / Putative type VI secretion system Rhs element Vgr / Type VI secretion system, RhsGE-associated Vgr family subset / Type VI secretion system, RhsGE-associated Vgr protein / Phage tail baseplate hub (GPD) / Gp5/Type VI secretion system Vgr protein, OB-fold domain ...Domain of unknown function DUF2235 / T6SS, Phospholipase effector Tle1-like, catalytic domain / Type VI secretion system spike protein VgrG2, C-terminal domain of unknown function DUF2345 / Putative type VI secretion system, Rhs element associated Vgr domain / Uncharacterized protein conserved in bacteria (DUF2345) / Putative type VI secretion system Rhs element Vgr / Type VI secretion system, RhsGE-associated Vgr family subset / Type VI secretion system, RhsGE-associated Vgr protein / Phage tail baseplate hub (GPD) / Gp5/Type VI secretion system Vgr protein, OB-fold domain / Type VI secretion system/phage-baseplate injector OB domain / Vgr protein, OB-fold domain superfamily / :
Similarity search - Domain/homology
Type VI secretion protein / Putative type VI secretion protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsRapisarda C / Fronzes R
Funding support France, Germany, 2 items
OrganizationGrant numberCountry
French National Research Agency France
European Communitys Seventh Framework Programme653706 Germany
CitationJournal: EMBO J / Year: 2020
Title: Structural basis for loading and inhibition of a bacterial T6SS phospholipase effector by the VgrG spike.
Authors: Nicolas Flaugnatti / Chiara Rapisarda / Martial Rey / Solène G Beauvois / Viet Anh Nguyen / Stéphane Canaan / Eric Durand / Julia Chamot-Rooke / Eric Cascales / Rémi Fronzes / Laure Journet /
Abstract: The bacterial type VI secretion system (T6SS) is a macromolecular machine that injects effectors into prokaryotic and eukaryotic cells. The mode of action of the T6SS is similar to contractile phages: ...The bacterial type VI secretion system (T6SS) is a macromolecular machine that injects effectors into prokaryotic and eukaryotic cells. The mode of action of the T6SS is similar to contractile phages: the contraction of a sheath structure pushes a tube topped by a spike into target cells. Effectors are loaded onto the spike or confined into the tube. In enteroaggregative Escherichia coli, the Tle1 phospholipase binds the C-terminal extension of the VgrG trimeric spike. Here, we purify the VgrG-Tle1 complex and show that a VgrG trimer binds three Tle1 monomers and inhibits their activity. Using covalent cross-linking coupled to high-resolution mass spectrometry, we provide information on the sites of contact and further identify the requirement for a Tle1 N-terminal secretion sequence in complex formation. Finally, we report the 2.6-Å-resolution cryo-electron microscopy tri-dimensional structure of the (VgrG) -(Tle1) complex revealing how the effector binds its cargo, and how VgrG inhibits Tle1 phospholipase activity. The inhibition of Tle1 phospholipase activity once bound to VgrG suggests that Tle1 dissociation from VgrG is required upon delivery.
History
DepositionAug 13, 2019-
Header (metadata) releaseApr 29, 2020-
Map releaseApr 29, 2020-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 6
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6sjl
  • Surface level: 6
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6sjl
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10218.png

Downloads & links

-
Map

FileDownload / File: emd_10218.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.02 Å/pix.
x 350 pix.
= 358.4 Å		1.02 Å/pix.
x 350 pix.
= 358.4 Å		1.02 Å/pix.
x 350 pix.
= 358.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.024 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.0 / Movie #1: 6
Minimum - Maximum-29.324508999999999 - 49.420203999999998
Average (Standard dev.)-0.000000000000692 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 358.40002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0241.0241.024
M x/y/z350350350
origin x/y/z0.0000.0000.000
length x/y/z358.400358.400358.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ350350350
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS350350350
D min/max/mean-29.32549.420-0.000

-
Supplemental data

-
Additional map: Unsharpened map

Fileemd_10218_additional.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map1

Fileemd_10218_half_map_1.map
AnnotationHalf map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map2

Fileemd_10218_half_map_2.map
AnnotationHalf map2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Tle1 effector bound to the VgrG spike of the type 6 secretion system

EntireName: Tle1 effector bound to the VgrG spike of the type 6 secretion system
Components
  • Complex: Tle1 effector bound to the VgrG spike of the type 6 secretion system
    • Protein or peptide: Putative type VI secretion protein
    • Protein or peptide: Putative type VI secretion protein

-
Supramolecule #1: Tle1 effector bound to the VgrG spike of the type 6 secretion system

SupramoleculeName: Tle1 effector bound to the VgrG spike of the type 6 secretion system
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 956 KDa

-
Macromolecule #1: Putative type VI secretion protein

MacromoleculeName: Putative type VI secretion protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 92.657219 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNLTDSLQNV LSGVGTLNRY RLDIPSCPSS LDVEDFSGTE GISKIYRYDI IFTSTDRYPD AAWFLRKSAT LIMGTGLLES LTEQKKVHG VITDFRRISG SEDQAQYRIT LKPFISLLDK QFRTHRFFVN KSVPEVVEQI LTEHGLKGWE YEFSLKRTYP K REQINQYQ ...String:
MNLTDSLQNV LSGVGTLNRY RLDIPSCPSS LDVEDFSGTE GISKIYRYDI IFTSTDRYPD AAWFLRKSAT LIMGTGLLES LTEQKKVHG VITDFRRISG SEDQAQYRIT LKPFISLLDK QFRTHRFFVN KSVPEVVEQI LTEHGLKGWE YEFSLKRTYP K REQINQYQ ESDLRFIQRL LAEVGIFYFF TLHPDAQTEV IHFGDVQAAL IFDKTLPVNS PSGMSDSGTD SVWALNVEHR VV ESRVITN DYNHREAQNI LMSVPADMTR GEGYDTSYGE VYHYRPRHTE RGDKIDPAPE TANFWARLDH ERFLAEQTRI TGK STDASL LPAQVLTITD STPPVLPAPL QEPVLLTQLL FTGSRKSALQ VMLSAVPYSE IVCWRPPLLT RPKITGTMTA RVTS AKEGD IYAWQDASGM YRVKFDADRD DKNPGQESMP VRLAKPYSGD AYGFHFPLIQ GTEVAIAFEE GDPDRPYIAH ALHDS RHVD HVTDKNGTRN VIRTPANNKL RMEDKRGEEH IKLSTEYGGK TQLNLGHNVD ASRELRGEGA ELRTDDWISI RGGKGI FIS ADMQPQAQGK MLDMDEAIRQ LEQALSLARS MAKAATAANA TQGDISCQQR LNASLTDLTA PGMLLHAPDG IGMVSAR AL RIASGSESVG IMSGDNTDIT AGQSFTVVAE GAVSLLSRNQ GMQLLAAKGR VNIQAQSDDL SMSSQQNLDI QSSEGKVT V SANQELILAC GGAYIKLSGG NIELGCPGQI LLKSTNMQKM GPTSLDIASV EMPRGFGGGF ILTDEAGVPQ PSTPYRLTT AEGDILQGIT DENGKTAPVN TSIPSVVKVE FGKVKIHGET E

UniProtKB: Putative type VI secretion protein

-
Macromolecule #2: Putative type VI secretion protein

MacromoleculeName: Putative type VI secretion protein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 62.422754 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTKYQGYDVT DATHKTSIHN DWKVVVAKKK PARGVTLTIG IFFDGTGNNR ENTASRLMKF NECSAARQGV NQKDAQSCED FLKEINKNS ISNGSYRGYY SNIHWLNILY HPDQVLKKDQ TSAQIKTYIS GIGTAAGEAD SVIGMGLGTS ILDIFEGVVT K TDEAMERI ...String:
MTKYQGYDVT DATHKTSIHN DWKVVVAKKK PARGVTLTIG IFFDGTGNNR ENTASRLMKF NECSAARQGV NQKDAQSCED FLKEINKNS ISNGSYRGYY SNIHWLNILY HPDQVLKKDQ TSAQIKTYIS GIGTAAGEAD SVIGMGLGTS ILDIFEGVVT K TDEAMERI TQALSEFMGF NLSPDFCIAK IQFDVFGFSR GAAAARHFAN RVMEQDPAIA RAIAKGLRGD FYDGKPSGEV RF LGLFDTV AAIGGISNFF DINGRSNPGV KLELRPSVAK KVFQITAMNE YRYNFSLNSI KGMWPELALP GAHSDIGGGY NPV GSPLQE NESLFLSCPE FEIVSDDTRE MDTRVYRKAE QVRKMLMTLP ALKHILPHGK LTTKIRSIGV NNSNQRRAGV IQKQ VGAAV FFERMAVPND WANVCLRVML DAAQEAGVLF EPIRQTNTEL QLPSELIFLA DKAIAQGKAV RLGQEPQAFT EEELY IIGK YTHCSANWNI ESDGNLWVDP TTGEIFIHRF GPKGNKAFVF PNKPNDRWIR SVWYMDDQQR LNDNAVKNTK VMMSGV

UniProtKB: Type VI secretion protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.6 mg/mL
BufferpH: 7.5
GridModel: UltrAuFoil / Material: GOLD / Mesh: 200
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 53.94 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 468438
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 2 / Software - Name: cryoSPARC

+
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