[English] 日本語
Yorodumi
- EMDB-2520: Injectisome in the tomogram of Salmonella mini-cell -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2520
TitleInjectisome in the tomogram of Salmonella mini-cell
Map dataSubtomogram averaged structure of Injectisome from Salmonella typhimurium
Sample
  • Sample: Injectisome from Salmonella typhimurium mini-cell in situ
  • Organelle or cellular component: type III secretion system
KeywordsInjectisome / Type III secretion system / Salmonella typhimurium / Mini-cell / Electron cryotomography
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 44.0 Å
AuthorsKawamoto A / Morimoto VY / Miyata T / Minamino T / Hughes TK / Kato T / Namba K
CitationJournal: Sci Rep / Year: 2013
Title: Common and distinct structural features of Salmonella injectisome and flagellar basal body.
Authors: Akihiro Kawamoto / Yusuke V Morimoto / Tomoko Miyata / Tohru Minamino / Kelly T Hughes / Takayuki Kato / Keiichi Namba /
Abstract: Bacterial pathogens use an injectisome to deliver virulence proteins into eukaryotic host cells. The bacterial flagellum and injectisome export their component proteins for self-assembly. These two ...Bacterial pathogens use an injectisome to deliver virulence proteins into eukaryotic host cells. The bacterial flagellum and injectisome export their component proteins for self-assembly. These two systems show high structural similarities and are classified as the type III secretion system, but it remains elusive how similar they are in situ because the structures of these complexes isolated from cells and visualized by electron cryomicroscopy have shown only the export channel and housing for the export apparatus. Here we report in situ structures of Salmonella injectisome and flagellum by electron cryotomography. The injectisome lacks the flagellar basal body C-ring, but a wing-like disc and a globular density corresponding to the export gate platform and ATPase hexamer ring, respectively, are stably attached through thin connectors, revealing yet unidentified common architectures of the two systems. The ATPase ring is far from the disc, suggesting that both apparatuses are observed in an export-off state.
History
DepositionNov 26, 2013-
Header (metadata) releaseDec 18, 2013-
Map releaseDec 25, 2013-
UpdateDec 25, 2013-
Current statusDec 25, 2013Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.237
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.237
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2520-1.png

Downloads & links

-
Map

FileDownload / File: emd_2520.map.gz / Format: CCP4 / Size: 2.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram averaged structure of Injectisome from Salmonella typhimurium
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
11.4 Å/pix.
x 82 pix.
= 934.8 Å		11.4 Å/pix.
x 82 pix.
= 934.8 Å		11.4 Å/pix.
x 82 pix.
= 934.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 11.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.237 / Movie #1: 0.237
Minimum - Maximum-2.02735949 - 5.20517445
Average (Standard dev.)0.01956169 (±0.89927512)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-767155240
Dimensions828282
Spacing828282
CellA=B=C: 934.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z11.411.411.4
M x/y/z828282
origin x/y/z0.0000.0000.000
length x/y/z934.800934.800934.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS155-767240
NC/NR/NS828282
D min/max/mean-2.0275.2050.020

-
Supplemental data

-
Sample components

-
Entire : Injectisome from Salmonella typhimurium mini-cell in situ

EntireName: Injectisome from Salmonella typhimurium mini-cell in situ
Components
  • Sample: Injectisome from Salmonella typhimurium mini-cell in situ
  • Organelle or cellular component: type III secretion system

-
Supramolecule #1000: Injectisome from Salmonella typhimurium mini-cell in situ

SupramoleculeName: Injectisome from Salmonella typhimurium mini-cell in situ
type: sample / ID: 1000 / Number unique components: 1
Molecular weightTheoretical: 3.5 MDa

-
Supramolecule #1: type III secretion system

SupramoleculeName: type III secretion system / type: organelle_or_cellular_component / ID: 1 / Name.synonym: injectisome / Recombinant expression: No
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Location in cell: Plasma membrane
Molecular weightTheoretical: 3.5 MDa

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

-
Sample preparation

BufferDetails: M9 medium (17.1g Na2HPO4-12H2O, 3g KH2PO4, 0.5g NaCl, 1g NH4Cl, 0.2%glycerol, 1% typtone, 1mM MgSO4 per litre)
GridDetails: Quantifoil molybdenum 200 mesh R0.6/1.0 grid with thin carbon support
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK II

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 80 K
DateDec 17, 2012
Image recordingCategory: CCD / Film or detector model: FEI FALCON I (4k x 4k) / Average electron dose: 200 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 49030 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 7.0 µm / Nominal defocus min: 4.0 µm / Nominal magnification: 29000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt series - Axis1 - Min angle: -70 ° / Tilt series - Axis1 - Max angle: 70 °
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionApplied symmetry - Point group: C24 (24 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 44.0 Å / Resolution method: OTHER / Software - Name: EMAN / Number subtomograms used: 75

+
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