[English] 日本語
Yorodumi
- EMDB-4898: TssA protein from T6SS of Vibrio cholerae. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-4898
TitleTssA protein from T6SS of Vibrio cholerae.
Map data
Sample
  • Complex: Type VI secretion system protein TssA.
    • Complex: Middle N-terminal domain (Nt2) of TssA protein from T6SS of Vibrio cholerae.
      • Protein or peptide: Type VI secretion system protein TssA
KeywordsT6SS / Vibrio / TssA / cap / TRANSPORT PROTEIN
Function / homologyType VI secretion system-associated, VCA0119 / Type VI secretion, EvfE, EvfF, ImpA, BimE, VC_A0119, VasJ / ImpA, N-terminal / ImpA, N-terminal, type VI secretion system / Type VI secretion system protein TssA / ImpA N-terminal domain-containing protein
Function and homology information
Biological speciesVibrio cholerae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsNazarov S / Adaixo R / Basler M
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science FoundationBSSGI0_155778 Switzerland
CitationJournal: EMBO J / Year: 2019
Title: Diverse roles of TssA-like proteins in the assembly of bacterial type VI secretion systems.
Authors: Johannes Paul Schneider / Sergey Nazarov / Ricardo Adaixo / Martina Liuzzo / Peter David Ringel / Henning Stahlberg / Marek Basler /
Abstract: Protein translocation by the bacterial type VI secretion system (T6SS) is driven by a rapid contraction of a sheath assembled around a tube with associated effectors. Here, we show that TssA-like or ...Protein translocation by the bacterial type VI secretion system (T6SS) is driven by a rapid contraction of a sheath assembled around a tube with associated effectors. Here, we show that TssA-like or TagA-like proteins with a conserved N-terminal domain and varying C-terminal domains can be grouped into at least three distinct classes based on their role in sheath assembly. The proteins of the first class increase speed and frequency of sheath assembly and form a stable dodecamer at the distal end of a polymerizing sheath. The proteins of the second class localize to the cell membrane and block sheath polymerization upon extension across the cell. This prevents excessive sheath polymerization and bending, which may result in sheath destabilization and detachment from its membrane anchor and thus result in failed secretion. The third class of these proteins localizes to the baseplate and is required for initiation of sheath assembly. Our work shows that while various proteins share a conserved N-terminal domain, their roles in T6SS biogenesis are fundamentally different.
History
DepositionApr 25, 2019-
Header (metadata) releaseAug 21, 2019-
Map releaseAug 21, 2019-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6riu
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6riu
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4898.png

Downloads & links

-
Map

FileDownload / File: emd_4898.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 324 pix.
= 342.792 Å		1.06 Å/pix.
x 324 pix.
= 342.792 Å		1.06 Å/pix.
x 324 pix.
= 342.792 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.058 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.008977853 - 0.04275847
Average (Standard dev.)0.000004379197 (±0.00118218)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions324324324
Spacing324324324
CellA=B=C: 342.792 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0581.0581.058
M x/y/z324324324
origin x/y/z0.0000.0000.000
length x/y/z342.792342.792342.792
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS324324324
D min/max/mean-0.0090.0430.000

-
Supplemental data

-
Mask #1

Fileemd_4898_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_4898_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #3

Fileemd_4898_additional_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #2

Fileemd_4898_additional_3.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_4898_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_4898_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Type VI secretion system protein TssA.

EntireName: Type VI secretion system protein TssA.
Components
  • Complex: Type VI secretion system protein TssA.
    • Complex: Middle N-terminal domain (Nt2) of TssA protein from T6SS of Vibrio cholerae.
      • Protein or peptide: Type VI secretion system protein TssA

-
Supramolecule #1: Type VI secretion system protein TssA.

SupramoleculeName: Type VI secretion system protein TssA. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 634 KDa

-
Supramolecule #2: Middle N-terminal domain (Nt2) of TssA protein from T6SS of Vibri...

SupramoleculeName: Middle N-terminal domain (Nt2) of TssA protein from T6SS of Vibrio cholerae.
type: complex / ID: 2 / Parent: 1 / Macromolecule list: all
Source (natural)Organism: Vibrio cholerae (bacteria)

-
Macromolecule #1: Type VI secretion system protein TssA

MacromoleculeName: Type VI secretion system protein TssA / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 53.102793 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MEMTEYRQCV AKPISSSNPV GERLVDHPLF DFIEDQMMKV GSLSHASVQW DEVEHSTLKL LGEQSKDIKL LVYLLQCLHN QVTPTRLIT SFAVMSEFLN QYWNDSYPAP GARGNLPRRK FFSQMAQRFT TVIEKFDFHH LDEADRQALQ AAVEEWQQAV E KQGLSSEL ...String:
MEMTEYRQCV AKPISSSNPV GERLVDHPLF DFIEDQMMKV GSLSHASVQW DEVEHSTLKL LGEQSKDIKL LVYLLQCLHN QVTPTRLIT SFAVMSEFLN QYWNDSYPAP GARGNLPRRK FFSQMAQRFT TVIEKFDFHH LDEADRQALQ AAVEEWQQAV E KQGLSSEL VESVVVRITA EIKRAEQRQQ VTAQSSAERE TPSAATSSPA ASMVVDHSSD KAAKQTLLKV ADFLAEQEFG IA LSIRLRR FAVWGSITSL PDHKPDGETL LRGMQADRVK DYQDQLRHPD LALWRKVEQS LTMAPYWFEG QWMSYTIAQQ LGK SDWCQA IAEETQQFLR RLPSLLELKF KGGEPFVSDS VKEWLASVGQ SQGAAGQSVG GDWQEKRKEA FQLAKEGGIA VALS MLNDG LVSAVEPRDK FYWRLLSADL LRANHLDAMA GEQYQTLLNQ VTTLSVPEWE PSLVEQIQRY TTSE

UniProtKB: Type VI secretion system protein TssA

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridMaterial: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: LACEY
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Details: Leica EM GP2.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 2963 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 261412
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 31781
Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

6g7c


Chain - Chain ID: A / Chain - Residue range: 388-474 / Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-6riu:
C-terminal domain of TssA protein from T6SS of Vibrio cholerae.

+
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