[English] 日本語
Yorodumi
- EMDB-2414: Signaling in Chemoreceptor Arrays Through Mobility Control of Kin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2414
TitleSignaling in Chemoreceptor Arrays Through Mobility Control of Kinase Domains - kinase activity state locked off - tsr mutant M222R
Map datasubvolume average of receptor array of tsr variant M222R
Sample
  • Sample: chemoreceptor array with receptor variant tsr M222R
  • Protein or peptide: tsr M222R
  • Protein or peptide: CheW
  • Protein or peptide: CheA
Keywordschemotaxis / E.coli / CheA
Biological speciesEscherichia coli (E. coli)
Methodsubtomogram averaging / cryo EM / Resolution: 30.0 Å
AuthorsBriegel A / Ames P / Gumbart JC / Oikonomou CM / Parkinson JS / Jensen GJ
CitationJournal: Mol Microbiol / Year: 2013
Title: The mobility of two kinase domains in the Escherichia coli chemoreceptor array varies with signalling state.
Authors: Ariane Briegel / Peter Ames / James C Gumbart / Catherine M Oikonomou / John S Parkinson / Grant J Jensen /
Abstract: Motile bacteria sense their physical and chemical environment through highly cooperative, ordered arrays of chemoreceptors. These signalling complexes phosphorylate a response regulator which in turn ...Motile bacteria sense their physical and chemical environment through highly cooperative, ordered arrays of chemoreceptors. These signalling complexes phosphorylate a response regulator which in turn governs flagellar motor reversals, driving cells towards favourable environments. The structural changes that translate chemoeffector binding into the appropriate kinase output are not known. Here, we apply high-resolution electron cryotomography to visualize mutant chemoreceptor signalling arrays in well-defined kinase activity states. The arrays were well ordered in all signalling states, with no discernible differences in receptor conformation at 2-3 nm resolution. Differences were observed, however, in a keel-like density that we identify here as CheA kinase domains P1 and P2, the phosphorylation site domain and the binding domain for response regulator target proteins. Mutant receptor arrays with high kinase activities all exhibited small keels and high proteolysis susceptibility, indicative of mobile P1 and P2 domains. In contrast, arrays in kinase-off signalling states exhibited a range of keel sizes. These findings confirm that chemoreceptor arrays do not undergo large structural changes during signalling, and suggest instead that kinase activity is modulated at least in part by changes in the mobility of key domains.
History
DepositionJul 9, 2013-
Header (metadata) releaseJul 17, 2013-
Map releaseJul 17, 2013-
UpdateMar 26, 2014-
Current statusMar 26, 2014Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 3.05
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

M222R.tif

Downloads & links

-
Map

FileDownload / File: emd_2414.map.gz / Format: CCP4 / Size: 825.2 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsubvolume average of receptor array of tsr variant M222R
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.44 Å/pix.
x 60 pix.
= 386.4 Å		6.44 Å/pix.
x 60 pix.
= 386.4 Å		6.44 Å/pix.
x 60 pix.
= 386.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.44 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.05 / Movie #1: 3.05
Minimum - Maximum1.28919983 - 4.03999996
Average (Standard dev.)2.81754231 (±0.32731485)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions606060
Spacing606060
CellA=B=C: 386.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.446.446.44
M x/y/z606060
origin x/y/z0.0000.0000.000
length x/y/z386.400386.400386.400
α/β/γ90.00090.00090.000
start NX/NY/NZ00-40
NX/NY/NZ555581
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS606060
D min/max/mean1.2894.0402.818

-
Supplemental data

-
Sample components

-
Entire : chemoreceptor array with receptor variant tsr M222R

EntireName: chemoreceptor array with receptor variant tsr M222R
Components
  • Sample: chemoreceptor array with receptor variant tsr M222R
  • Protein or peptide: tsr M222R
  • Protein or peptide: CheW
  • Protein or peptide: CheA

-
Supramolecule #1000: chemoreceptor array with receptor variant tsr M222R

SupramoleculeName: chemoreceptor array with receptor variant tsr M222R / type: sample / ID: 1000 / Number unique components: 3

-
Macromolecule #1: tsr M222R

MacromoleculeName: tsr M222R / type: protein_or_peptide / ID: 1 / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)

-
Macromolecule #2: CheW

MacromoleculeName: CheW / type: protein_or_peptide / ID: 2 / Recombinant expression: No
Source (natural)Organism: Escherichia coli (E. coli)

-
Macromolecule #3: CheA

MacromoleculeName: CheA / type: protein_or_peptide / ID: 3 / Oligomeric state: dimer / Recombinant expression: No
Source (natural)Organism: Escherichia coli (E. coli)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

-
Sample preparation

BufferDetails: Tryptone Broth (10 g/L Tryptone, 5 g/L NaCl). Cells were incubated with penicillin for 1 hour prior to freezing.
GridDetails: R 2/2 copper/rhodium grids, glow discharged
VitrificationCryogen name: ETHANE-PROPANE MIXTURE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III

-
Electron microscopy

MicroscopeFEI POLARA 300
Specialist opticsEnergy filter - Name: FEI / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
DateNov 1, 2011
Image recordingAverage electron dose: 150 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus min: 10.0 µm / Nominal magnification: 34000
Sample stageSpecimen holder model: OTHER / Tilt series - Axis1 - Min angle: -66.93 ° / Tilt series - Axis1 - Max angle: 59.52 °
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

-
Image processing

DetailsCTF-corrected. Average number of tilts used in the 3D reconstructions: 128. Average tomographic tilt angle increment: 1.
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: OTHER / Software - Name: IMOD, tomo3D / Number subtomograms used: 96
CTF correctionDetails: IMOD

+
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