[English] 日本語
Yorodumi
- EMDB-0009: The baseplate complex from the type VI secretion system -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0009
TitleThe baseplate complex from the type VI secretion system
Map data
Sample
  • Complex: Type VI secretion system baseplate complexType VI secretion system
    • Protein or peptide: Putative type VI secretion proteinType VI secretion system
    • Protein or peptide: TssG
    • Protein or peptide: TssE
Function / homology
Function and homology information


Type VI secretion system protein TssE1-like / Type VI secretion system TssF / Type VI secretion system, TssF / Type VI secretion, TssG-like / Type VI secretion, TssG / IraD/Gp25-like / Baseplate wedge protein gp25
Similarity search - Domain/homology
GPW_gp25 domain-containing protein / Type VI secretion system baseplate subunit TssG / Type VI secretion system baseplate subunit TssF / Type VI secretion protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsRapisarda C / Fronzes R
CitationJournal: Nat Microbiol / Year: 2018
Title: Biogenesis and structure of a type VI secretion baseplate.
Authors: Yassine Cherrak / Chiara Rapisarda / Riccardo Pellarin / Guillaume Bouvier / Benjamin Bardiaux / Fabrice Allain / Christian Malosse / Martial Rey / Julia Chamot-Rooke / Eric Cascales / Rémi ...Authors: Yassine Cherrak / Chiara Rapisarda / Riccardo Pellarin / Guillaume Bouvier / Benjamin Bardiaux / Fabrice Allain / Christian Malosse / Martial Rey / Julia Chamot-Rooke / Eric Cascales / Rémi Fronzes / Eric Durand /
Abstract: To support their growth in a competitive environment and cause pathogenesis, bacteria have evolved a broad repertoire of macromolecular machineries to deliver specific effectors and toxins. Among ...To support their growth in a competitive environment and cause pathogenesis, bacteria have evolved a broad repertoire of macromolecular machineries to deliver specific effectors and toxins. Among these multiprotein complexes, the type VI secretion system (T6SS) is a contractile nanomachine that targets both prokaryotic and eukaryotic cells. The T6SS comprises two functional subcomplexes: a bacteriophage-related tail structure anchored to the cell envelope by a membrane complex. As in other contractile injection systems, the tail is composed of an inner tube wrapped by a sheath and built on the baseplate. In the T6SS, the baseplate is not only the tail assembly platform, but also docks the tail to the membrane complex and hence serves as an evolutionary adaptor. Here we define the biogenesis pathway and report the cryo-electron microscopy (cryo-EM) structure of the wedge protein complex of the T6SS from enteroaggregative Escherichia coli (EAEC). Using an integrative approach, we unveil the molecular architecture of the whole T6SS baseplate and its interaction with the tail sheath, offering detailed insights into its biogenesis and function. We discuss architectural and mechanistic similarities but also reveal key differences with the T4 phage and Mu phage baseplates.
History
DepositionMay 15, 2018-
Header (metadata) releaseJun 20, 2018-
Map releaseOct 17, 2018-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 4.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6gj1
  • Surface level: 4.5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_0009.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 4.5 / Movie #1: 4.5
Minimum - Maximum-9.079956 - 16.808065
Average (Standard dev.)-0.00000000000 (±1)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 220.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z220.000220.000220.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ200200200
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-9.08016.808-0.000

-
Supplemental data

-
Sample components

-
Entire : Type VI secretion system baseplate complex

EntireName: Type VI secretion system baseplate complexType VI secretion system
Components
  • Complex: Type VI secretion system baseplate complexType VI secretion system
    • Protein or peptide: Putative type VI secretion proteinType VI secretion system
    • Protein or peptide: TssG
    • Protein or peptide: TssE

-
Supramolecule #1: Type VI secretion system baseplate complex

SupramoleculeName: Type VI secretion system baseplate complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

-
Macromolecule #1: Putative type VI secretion protein

MacromoleculeName: Putative type VI secretion protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 66.557125 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MDDLTLRYFD AEMRYLREAG KAFAQAHPDR AAMLDLDKAG TPDPCVERLF EGFAFSMGRL RQKIDDDLPE LTESLVSMLW PHYLRTIPS LSVVALTPRL SVMKMAETVP AGLEVTSRPV GPGNTVCRYR TTRAIPLNPL AVEKVVMTTE PDGRSVLKIG F ACSELADW ...String:
MDDLTLRYFD AEMRYLREAG KAFAQAHPDR AAMLDLDKAG TPDPCVERLF EGFAFSMGRL RQKIDDDLPE LTESLVSMLW PHYLRTIPS LSVVALTPRL SVMKMAETVP AGLEVTSRPV GPGNTVCRYR TTRAIPLNPL AVEKVVMTTE PDGRSVLKIG F ACSELADW SQVDLHRLSL YLAAEAPVSS TLHLMMTKRL AALYLRLPGN DERIRIDGWF SPGGFAEEDR LWPKGDSAFS GY QLLLEYF TFREKFMFVH LNGLENVSLP AGISGFDLEV VLSQPWPADL PVTDDALCLH CVPVINLFTL EADPLIINGL ESE YLLRPK RLQDGYTEIY SVDAVTGSGR TGSAEYVPFT SFRHRGGMLR HDAPERYYHT RVKRGVTGMY DTWLILGGQR WEAD RMPER ETLSLRITGT NGQLPRRALQ STLLDRCEQV LQAPVSVRNL CKPTLPVYPP TEDRFHWRVM SHLGTGFLNM LSSAE VLRG TLALYNWRDD ELNHRRLDAI LAVQHHRIQR FEKGFLLRGL DVEVTLDGNG FAGEGDIHLF GEMLNRFLAL YADMNQ FNQ LTLIVQPEGK CIRWKENHNP RLPG

-
Macromolecule #2: TssG

MacromoleculeName: TssG / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 41.216344 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MHPVERKSQS APARLITRYR KQLPYINFYR FCQLLEQSQP DQPPIGSGWQ ARQEAVRFCP YPGMGFPASE IKDAVIPEES HLPPIVHVT FMGLYGVTSP LPAHYISDIA QQREGHEAAA DFLDIFSHRL ITQYYRIWRK YSYPATFEAG GQDKTSQYLL G LARLGIPG ...String:
MHPVERKSQS APARLITRYR KQLPYINFYR FCQLLEQSQP DQPPIGSGWQ ARQEAVRFCP YPGMGFPASE IKDAVIPEES HLPPIVHVT FMGLYGVTSP LPAHYISDIA QQREGHEAAA DFLDIFSHRL ITQYYRIWRK YSYPATFEAG GQDKTSQYLL G LARLGIPG CAQNIATPVS RFLALLPLML LPGRTAEGLT SLVTLLAPGT QARVWHHDRR RIPLKTPLTM RVHHPVSLKS RP VMGDHAT DVNGQVLLQL STQTGSEVQG WLPGGHLYSD LLALLHVYLG SRLDVRLQLC VERSLLPDAR LSCRPAAGSP QLG RTAVMR TQAKIATSAA RVMTISLGRY QRVQEHYQRK ETQENGDYRW

-
Macromolecule #3: TssE

MacromoleculeName: TssE / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 16.320783 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MPRPSLYEIL YGNFTGGLEL NQVGEEEQVI LSVLDNMQRI LNTRAGSLKH LPDYGLPDIT TILQGMPGTA HQLMRVLSDV LLKYEPRIK RVDVTMQEQT QPGELHYVID AELKDAGLVR YGTTFIPEGR VLLRHLKQQR YVQT

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

CTF correctionSoftware - Name: Gctf
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 32504

+
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