[English] 日本語
Yorodumi
- EMDB-0464: Legionella pneumophila bacterial flagellar motor -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 0464
TitleLegionella pneumophila bacterial flagellar motor
Map dataem-volume_P1
SampleLegionella pneumophila bacterial flagellar motor:
SourceLegionella pneumophila (bacteria)
Methodsubtomogram averaging / cryo EM / 64 Å resolution
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 ...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 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
DateDeposition: Jan 15, 2019 / Header (metadata) release: Jan 30, 2019 / Map release: Jan 30, 2019 / Last update: Jan 30, 2019

-
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_0464.png

Downloads & links

-
Map

Fileemd_0464.map.gz (map file in CCP4 format, 701 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
50 pix
15.6 Å/pix.
= 780. Å		70 pix
15.6 Å/pix.
= 1092. Å		50 pix
15.6 Å/pix.
= 780. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 15.6 Å
Density

Histogram

Histogram (log scale)
Contour Level:179.0 (by author), 179 (movie #1):
Minimum - Maximum0.0 - 255.0
Average (Standard dev.)134.840480000000014 (49.389496000000001)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions705050
Origin0.00.00.0
Limit69.049.049.0
Spacing507050
CellA: 780.0 Å / B: 1092.0 Å / C: 780.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z15.615.615.6
M x/y/z507050
origin x/y/z0.0000.0000.000
length x/y/z780.0001092.000780.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS507050
D min/max/mean0.000255.000134.840

-
Supplemental data

-
Sample components

-
Entire Legionella pneumophila bacterial flagellar motor

EntireName: Legionella pneumophila bacterial flagellar motor / Number of components: 1

-
Component #1: protein, Legionella pneumophila bacterial flagellar motor

ProteinName: Legionella pneumophila bacterial flagellar motor / Recombinant expression: No
SourceSpecies: Legionella pneumophila (bacteria)

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: cell / Method: cryo EM
Sample solutionpH: 6.9
VitrificationCryogen name: OTHER

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.2 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C2 (2 fold cyclic) / Number of subtomograms: 44
3D reconstructionSoftware: IMOD, TOMO3D, PEET / Resolution: 64 Å / Resolution method: FSC 0.143 CUT-OFF

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at EBI / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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