[English] 日本語
Yorodumi
- EMDB-6093: Electron cryo-tomography of flagellar motor from Borrelia burgdor... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-6093
TitleElectron cryo-tomography of flagellar motor from Borrelia burgdorferi (FliR mutant)
Map dataReconstruction of mutant of Borrelia burgdorferi flagellar motor (FliR mutant)
Sample
  • Sample: Flagellar motor mutant from Borrelia burgdorferi (FliR mutant)
  • Organelle or cellular component: flagellar motor
KeywordsFliR / type III secretion / flagellar motor / Borrelia burgdorferi / ATPase
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
Methodsubtomogram averaging / cryo EM / Resolution: 41.0 Å
AuthorsTu JG / Zhao XW / Manne A / Lees K / Yerke A / Zhang K / Li CH / Norris SJ / Motaleb MA / Liu J
CitationJournal: To Be Published
Title: Molecular architecture and secretion mechanism of the flagellar type III secretion machine in Borrelia burgdorferi
Authors: Tu JG / Zhao XW / Manne A / Lees K / Yerke A / Zhang K / Li CH / Norris SJ / Motaleb MA / Liu J
History
DepositionSep 14, 2014-
Header (metadata) releaseOct 8, 2014-
Map releaseSep 30, 2015-
UpdateSep 30, 2015-
Current statusSep 30, 2015Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.96
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.96
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6093.jpg

Downloads & links

-
Map

FileDownload / File: emd_6093.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of mutant of Borrelia burgdorferi flagellar motor (FliR mutant)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.6 Å/pix.
x 256 pix.
= 1433.6 Å		5.6 Å/pix.
x 256 pix.
= 1433.6 Å		5.6 Å/pix.
x 256 pix.
= 1433.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.6 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.96 / Movie #1: 1.96
Minimum - Maximum-15.31581783 - 17.033920290000001
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 1433.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.65.65.6
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z1433.6001433.6001433.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-128-128-128
NC/NR/NS256256256
D min/max/mean-15.31617.0340.000

-
Supplemental data

-
Sample components

-
Entire : Flagellar motor mutant from Borrelia burgdorferi (FliR mutant)

EntireName: Flagellar motor mutant from Borrelia burgdorferi (FliR mutant)
Components
  • Sample: Flagellar motor mutant from Borrelia burgdorferi (FliR mutant)
  • Organelle or cellular component: flagellar motor

-
Supramolecule #1000: Flagellar motor mutant from Borrelia burgdorferi (FliR mutant)

SupramoleculeName: Flagellar motor mutant from Borrelia burgdorferi (FliR mutant)
type: sample / ID: 1000 / Number unique components: 1

-
Supramolecule #1: flagellar motor

SupramoleculeName: flagellar motor / type: organelle_or_cellular_component / ID: 1 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Borrelia burgdorferi (Lyme disease spirochete)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

-
Sample preparation

VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

-
Electron microscopy

MicroscopeFEI POLARA 300
DateAug 6, 2013
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k)
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 8.0 µm / Nominal defocus min: 6.0 µm / Nominal magnification: 31000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -64 ° / Tilt series - Axis1 - Max angle: 64 °
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

-
Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 41.0 Å / Resolution method: OTHER / Software - Name: IMOD, Protomo / Number subtomograms used: 830

+
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