[English] 日本語
Yorodumi
- EMDB-9341: Structure of the type VI secretion system TssK-TssF-TssG baseplat... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-9341
TitleStructure of the type VI secretion system TssK-TssF-TssG baseplate subcomplex revealed by cryo-electron microscopy - full map sharpenedType VI secretion system
Map dataType VI secretion system TssK-TssF-TssG baseplate subcomplex, sharpened mapType VI secretion system
Sample
  • Complex: TssK-TssF-TssG T6SS baseplate subcomplex
    • Protein or peptide: Putative type VI secretion proteinType VI secretion system
    • Protein or peptide: Putative type VI secretion proteinType VI secretion system
    • Protein or peptide: Unassigned protein
    • Protein or peptide: Putative type VI secretion proteinType VI secretion system
KeywordsType VI secretion system / enteroaggregative E. coli / protein secretion / baseplate / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / PROTEIN TRANSPORT
Function / homologyType VI secretion system TssF / Type VI secretion system, TssF / Type VI secretion, TssG-like / Type VI secretion, TssG / Type VI secretion system TssK / Bacterial Type VI secretion, VC_A0110, EvfL, ImpJ, VasE / Type VI secretion protein / Type VI secretion protein / Putative type VI secretion protein
Function and homology information
Biological speciesEscherichia coli O44:H18 (strain 042 / EAEC) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsPark YJ / Lacourse KD / Cambillau C / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / DiMaio F / Mougous JD / Veesler D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
CitationJournal: Nat Commun / Year: 2018
Title: Structure of the type VI secretion system TssK-TssF-TssG baseplate subcomplex revealed by cryo-electron microscopy.
Authors: Young-Jun Park / Kaitlyn D Lacourse / Christian Cambillau / Frank DiMaio / Joseph D Mougous / David Veesler /
Abstract: Type VI secretion systems (T6SSs) translocate effectors into target cells and are made of a contractile sheath and a tube docked onto a multi-protein transmembrane complex via a baseplate. Although ...Type VI secretion systems (T6SSs) translocate effectors into target cells and are made of a contractile sheath and a tube docked onto a multi-protein transmembrane complex via a baseplate. Although some information is available about the mechanisms of tail contraction leading to effector delivery, the detailed architecture and function of the baseplate remain unknown. Here, we report the 3.7 Å resolution cryo-electron microscopy reconstruction of an enteroaggregative Escherichia coli baseplate subcomplex assembled from TssK, TssF and TssG. The structure reveals two TssK trimers interact with a locally pseudo-3-fold symmetrical complex comprising two copies of TssF and one copy of TssG. TssF and TssG are structurally related to each other and to components of the phage T4 baseplate and of the type IV secretion system, strengthening the evolutionary relationships among these macromolecular machines. These results, together with bacterial two-hybrid assays, provide a structural framework to understand the T6SS baseplate architecture.
History
DepositionNov 14, 2018-
Header (metadata) releaseDec 12, 2018-
Map releaseDec 26, 2018-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6n38
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9341.png

Downloads & links

-
Map

FileDownload / File: emd_9341.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationType VI secretion system TssK-TssF-TssG baseplate subcomplex, sharpened map
Voxel sizeX=Y=Z: 1.37 Å
Density
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.094658144 - 0.18709746
Average (Standard dev.)0.00016524785 (±0.0030255886)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 394.56 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.371.371.37
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z394.560394.560394.560
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.0950.1870.000

-
Supplemental data

-
Additional map: Type VI secretion system TssK-TssF-TssG baseplate subcomplex, unsharpened...

Fileemd_9341_additional.map
AnnotationType VI secretion system TssK-TssF-TssG baseplate subcomplex, unsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : TssK-TssF-TssG T6SS baseplate subcomplex

EntireName: TssK-TssF-TssG T6SS baseplate subcomplex
Components
  • Complex: TssK-TssF-TssG T6SS baseplate subcomplex
    • Protein or peptide: Putative type VI secretion proteinType VI secretion system
    • Protein or peptide: Putative type VI secretion proteinType VI secretion system
    • Protein or peptide: Unassigned protein
    • Protein or peptide: Putative type VI secretion proteinType VI secretion system

-
Supramolecule #1: TssK-TssF-TssG T6SS baseplate subcomplex

SupramoleculeName: TssK-TssF-TssG T6SS baseplate subcomplex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli O44:H18 (strain 042 / EAEC) (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 O44:H18 (strain 042 / EAEC) (bacteria)
Strain: 042 / EAEC
Molecular weightTheoretical: 66.557125 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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

UniProtKB: 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: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli O44:H18 (strain 042 / EAEC) (bacteria)
Strain: 042 / EAEC
Molecular weightTheoretical: 33.787875 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGFPASEIKD AVIPEESHLP PIVHVTFMGL YGVTSPLPAH YISDIAQQRE GHEAAADFLD IFSHRLITQY YRIWRKYSYP ATFEAGGQD KTSQYLLGLA RLGIPGCAQN IATPVSRFLA LLPLMLLPGR TAEGLTSLVT LLAPGTQARV WHHDRRRIPL K TPLTMRVH ...String:
MGFPASEIKD AVIPEESHLP PIVHVTFMGL YGVTSPLPAH YISDIAQQRE GHEAAADFLD IFSHRLITQY YRIWRKYSYP ATFEAGGQD KTSQYLLGLA RLGIPGCAQN IATPVSRFLA LLPLMLLPGR TAEGLTSLVT LLAPGTQARV WHHDRRRIPL K TPLTMRVH HPVSLKSRPV MGDHATDVNG QVLLQLSTQT GSEVQGWLPG GHLYSDLLAL LHVYLGSRLD VRLQLCVERS LL PDARLSC RPAAGSPQLG RTAVMRTQAK IATSAARVMT ISLGRYQRVQ EHYQRKETQE NGDYRW

UniProtKB: Putative type VI secretion protein

-
Macromolecule #3: Unassigned protein

MacromoleculeName: Unassigned protein / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli O44:H18 (strain 042 / EAEC) (bacteria)
Strain: strain 042 / EAEC
Molecular weightTheoretical: 1.805216 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)

-
Macromolecule #4: Putative type VI secretion protein

MacromoleculeName: Putative type VI secretion protein / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli O44:H18 (strain 042 / EAEC) (bacteria)
Strain: 042 / EAEC
Molecular weightTheoretical: 36.57768 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKIYRPLWED GAFLMPQQFQ QQAAWDVHLA DSVARMGLAH PWGVVAAEFD DSLLPLSRLN ATRLIVRFPD GTLIDTERAD NLPPVCDLS TVSDRSLVDI VLALPLLNAN GGNLDNGSES ERPRRWKSER VNVQELAGHE QSEVAVLRHN LTLRMAHQEN A AWLTCPVT ...String:
MKIYRPLWED GAFLMPQQFQ QQAAWDVHLA DSVARMGLAH PWGVVAAEFD DSLLPLSRLN ATRLIVRFPD GTLIDTERAD NLPPVCDLS TVSDRSLVDI VLALPLLNAN GGNLDNGSES ERPRRWKSER VNVQELAGHE QSEVAVLRHN LTLRMAHQEN A AWLTCPVT RLVRDAQGQW CRDPRFIPPL LTLSASPSLM TELAELLHHL QARRQRLMSM RRENNARLAD FAVADVSLFW LL NALNSAE PVLKELLDMP YRHPELLYRE LARLAGSLLT FSLEHNVDAV PAYHHETPEN VFPPLLSLLN RLLEASLPSH HHH HH

UniProtKB: Type VI secretion protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.12 mg/mL
BufferpH: 7.8
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
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) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: OTHER
Details: An initial model was obtained using cryosparc abinitio.
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 36496

+
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