[English] 日本語
Yorodumi
- EMDB-3813: Tomogram of the salmonella enterica wild-type bacterial flagellar... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 3813
TitleTomogram of the salmonella enterica wild-type bacterial flagellar motor
SampleSalmonella enterica Flagellar motor
SourceSalmonella / bacteria
Map data
Methodelectron tomography
AuthorsBeeby M / Ribardo DA / Brennan CA / Ruby EG / Jensen GJ / Hendrixson DR
CitationProc. Natl. Acad. Sci. U.S.A., 2016, 113, E1917-E1926

Proc. Natl. Acad. Sci. U.S.A., 2016, 113, E1917-E1926 Yorodumi Papers
Diverse high-torque bacterial flagellar motors assemble wider stator rings using a conserved protein scaffold.
Morgan Beeby / Deborah A Ribardo / Caitlin A Brennan / Edward G Ruby / Grant J Jensen / David R Hendrixson

DateDeposition: Jul 14, 2017 / Header (metadata) release: Jul 26, 2017 / Map release: Jul 26, 2017 / Last update: Aug 2, 2017

-
Structure visualization

Movie
  • Simplified surface model
  • Imaged by Jmol
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide
Supplemental images

Downloads & links

-
Map

Fileemd_3813.map.gz (map file in CCP4 format, 419431 KB)
Voxel sizeX=Y=Z: 8.122 Å
Density
Contour Level:52 (by author)
Minimum - Maximum-128 - 127
Average (Standard dev.)56.306488 (8.228934)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions10241024400
Origin00-400
Limit10231023-1
Spacing10241024400
CellA: 8316.928 Å / B: 8316.928 Å / C: 3248.7998 Å
α=β=γ: 90 deg.

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z8.1228.1228.122
M x/y/z10241024400
origin x/y/z0.0000.0000.000
length x/y/z8316.9288316.9283248.800
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS00-400
NC/NR/NS10241024400
D min/max/mean-128.000127.00056.306

-
Supplemental data

-
Sample components

-
Entire Salmonella enterica Flagellar motor

EntireName: Salmonella enterica Flagellar motor / Number of components: 1

-
Component #1: cellular-component, Salmonella enterica Flagellar motor

Cellular-componentName: Salmonella enterica Flagellar motor / Recombinant expression: No
SourceSpecies: Salmonella / bacteria / Strain: TH16943
Source (natural)Location in cell: Cell wall

-
Experimental details

-
Sample preparation

Specimen statecell
Sample solutionBuffer solution: PH is not know. PH of 7 was added because PH is a mandatory item.
pH: 7
Support filmQuantifoil R2/2 grids (200-mesh) (Quantifoil Micro Tools GmbH) were glow-discharged for 60 s at 10 mA.
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE-PROPANE MIXTURE / Humidity: 100 %

-
Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 0.6 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 4000 - 10000 nm
Specimen HolderModel: GATAN LIQUID NITROGEN / Tilt Angle: -61 - 61 deg.
CameraDetector: FEI FALCON II (4k x 4k)

-
Image processing

ProcessingMethod: electron tomography / Tilt angle increment: 3 deg. / Number of sections: 201
3D reconstructionSoftware: IMOD, RAPTOR, Leginon / Resolution method: OTHER

+
About Yorodumi

-
News

-
Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

-
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 / EM Navigator (legacy version) / Yorodumi (legacy version)

+
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 / EM Navigator (legacy version) / Yorodumi (legacy version)

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more