[English] 日本語
Yorodumi
- EMDB-10000: Lateral flagellar motor from Plesiomonas shigelloidea -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10000
TitleLateral flagellar motor from Plesiomonas shigelloidea
Map dataPlesiomonas shigelloides latreal flagellar motor
Sample
  • Complex: Lateral flagellar motor from Plesiomonas shigelloides
Biological speciesPlesiomonas shigelloides (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 120.0 Å
AuthorsFerreira JL / Beeby M
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/P019374/1 United Kingdom
Medical Research Council (United Kingdom)MR/K501281/1 United Kingdom
CitationJournal: Front Microbiol / Year: 2021
Title: The "Jack-of-all-Trades" Flagellum From and Was Horizontally Acquired From an Ancestral β-Proteobacterium.
Authors: Josie L Ferreira / Izaak Coleman / Max L Addison / Tobias Zachs / Bonnie L Quigley / Kristin Wuichet / Morgan Beeby /
Abstract: The γ-proteobacteria are a group of diverse bacteria including pathogenic , and species. The majority swim in liquids with polar, sodium-driven flagella and swarm on surfaces with lateral, non- ...The γ-proteobacteria are a group of diverse bacteria including pathogenic , and species. The majority swim in liquids with polar, sodium-driven flagella and swarm on surfaces with lateral, non-chemotactic flagella. Notable exceptions are the enteric Enterobacteriaceae such as and . Many of the well-studied Enterobacteriaceae are gut bacteria that both swim and swarm with the same proton-driven peritrichous flagella. How different flagella evolved in closely related lineages, however, has remained unclear. Here, we describe our phylogenetic finding that Enterobacteriaceae flagella are not native polar or lateral γ-proteobacterial flagella but were horizontally acquired from an ancestral β-proteobacterium. Using electron cryo-tomography and subtomogram averaging, we confirmed that Enterobacteriaceae flagellar motors resemble contemporary β-proteobacterial motors and are distinct to the polar and lateral motors of other γ-proteobacteria. Structural comparisons support a model in which γ-proteobacterial motors have specialized, suggesting that acquisition of a β-proteobacterial flagellum may have been beneficial as a general-purpose motor suitable for adjusting to diverse conditions. This acquisition may have played a role in the development of the enteric lifestyle.
History
DepositionMay 23, 2019-
Header (metadata) releaseDec 16, 2020-
Map releaseDec 16, 2020-
UpdateMay 5, 2021-
Current statusMay 5, 2021Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.11
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.11
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10000.png

Downloads & links

-
Map

FileDownload / File: emd_10000.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPlesiomonas shigelloides latreal flagellar motor
Voxel sizeX=Y=Z: 8.28 Å
Density
Contour LevelBy AUTHOR: 0.013 / Movie #1: 0.11
Minimum - Maximum-0.55448806 - 0.667116
Average (Standard dev.)0.016991854 (±0.13127448)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-20-10-10
Dimensions100100100
Spacing100100100
CellA=B=C: 828.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z8.288.288.28
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z828.000828.000828.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-10-20-10
NC/NR/NS100100100
D min/max/mean-0.5540.6670.017

-
Supplemental data

-
Sample components

-
Entire : Lateral flagellar motor from Plesiomonas shigelloides

EntireName: Lateral flagellar motor from Plesiomonas shigelloides
Components
  • Complex: Lateral flagellar motor from Plesiomonas shigelloides

-
Supramolecule #1: Lateral flagellar motor from Plesiomonas shigelloides

SupramoleculeName: Lateral flagellar motor from Plesiomonas shigelloides / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Plesiomonas shigelloides (bacteria)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

-
Sample preparation

BufferpH: 7 / Details: LB
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV
DetailsCells grown to OD600 0.6 in LB, lysed with penicillin G

-
Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 25000
Sample stageSpecimen holder model: GATAN 914 HIGH TILT LIQUID NITROGEN CRYO TRANSFER TOMOGRAPHY HOLDER
Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 6 / Average exposure time: 0.8 sec. / Average electron dose: 120.0 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

ExtractionNumber tomograms: 200 / Number images used: 220
Final angle assignmentType: OTHER
Final reconstructionApplied symmetry - Point group: C100 (100 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 120.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PEET / Number subtomograms used: 317

+
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