[English] 日本語
Yorodumi
- EMDB-0465: Pseudomonas aeruginosa bacterial flagellar motor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0465
TitlePseudomonas aeruginosa bacterial flagellar motor
Map dataem-volume_P1
Sample
  • Cell: Pseudomonas aeruginosa
Biological speciesPseudomonas aeruginosa (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 59.0 Å
AuthorsKaplan M / Ghosal D / Subramanian P / Oikonomou CO / Kjaer A / Pirbadian S / Ortega DR / Briegel A / El-Naggar MY / Jensen GJ
Citation
Journal: Elife / Year: 2019
Title: The presence and absence of periplasmic rings in bacterial flagellar motors correlates with stator type.
Authors: Mohammed Kaplan / Debnath Ghosal / Poorna Subramanian / Catherine M Oikonomou / Andreas Kjaer / Sahand Pirbadian / Davi R Ortega / Ariane Briegel / Mohamed Y El-Naggar / Grant J Jensen /
Abstract: The bacterial flagellar motor, a cell-envelope-embedded macromolecular machine that functions as a cellular propeller, exhibits significant structural variability between species. Different torque- ...The bacterial flagellar motor, a cell-envelope-embedded macromolecular machine that functions as a cellular propeller, exhibits significant structural variability between species. Different torque-generating stator modules allow motors to operate in different pH, salt or viscosity levels. How such diversity evolved is unknown. Here, we use electron cryo-tomography to determine the in situ macromolecular structures of three Gammaproteobacteria motors: , , and , providing the first views of intact motors with dual stator systems. Complementing our imaging with bioinformatics analysis, we find a correlation between the motor's stator system and its structural elaboration. Motors with a single H-driven stator have only the core periplasmic P- and L-rings; those with dual H-driven stators have an elaborated P-ring; and motors with Na or Na/H-driven stators have both their P- and L-rings embellished. Our results suggest an evolution of structural elaboration that may have enabled pathogenic bacteria to colonize higher-viscosity environments in animal hosts.
#1: Journal: bioRxiv
Title: The structural complexity of the Gammaproteobacteria flagellar motor is related to the type of its torque-generating stators
Authors: kaplan M / Ghosal D / Subramanian P / Oikonomou CO / Kjaer A / Pirbadian S / Ortega DR / El-Naggar MY / Jensen GJ
History
DepositionJan 15, 2019-
Header (metadata) releaseJan 30, 2019-
Map releaseJan 30, 2019-
UpdateJan 30, 2019-
Current statusJan 30, 2019Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 179
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 179
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0465.png

Downloads & links

-
Map

FileDownload / File: emd_0465.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationem-volume_P1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
13.06 Å/pix.
x 70 pix.
= 914.2 Å		13.06 Å/pix.
x 100 pix.
= 1306. Å		13.06 Å/pix.
x 70 pix.
= 914.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 13.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 179.0 / Movie #1: 179
Minimum - Maximum0.0 - 255.0
Average (Standard dev.)141.957439999999991 (±43.699986000000003)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions1007070
Spacing7010070
CellA: 914.2 Å / B: 1306.0 Å / C: 914.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z13.0613.0613.06
M x/y/z7010070
origin x/y/z0.0000.0000.000
length x/y/z914.2001306.000914.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS7010070
D min/max/mean0.000255.000141.957

-
Supplemental data

-
Sample components

-
Entire : Pseudomonas aeruginosa

EntireName: Pseudomonas aeruginosa (bacteria)
Components
  • Cell: Pseudomonas aeruginosa

-
Supramolecule #1: Pseudomonas aeruginosa

SupramoleculeName: Pseudomonas aeruginosa / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

-
Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE-PROPANE

-
Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

-
Image processing

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 59.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 144
ExtractionNumber tomograms: 156 / Number images used: 144
Final angle assignmentType: OTHER

+
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