[English] 日本語
Yorodumi
- EMDB-15643: Native Chemotaxis Core Signalling Complex from E. coli, Focused a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-15643
TitleNative Chemotaxis Core Signalling Complex from E. coli, Focused alignment on ligand binding domain
Map dataNative Chemotaxis Core Signalling Complex in E. coli, focused alignment on the ligand binding domain, cubic map, unfiltered, unmasked
Sample
  • Complex: Native Chemotaxis Core Signalling Complex
KeywordsChemotaxis Core Signalling Complex from E. coli / Chemotaxis / Signal Transduction / Chemoreceptor / Core signaling complex / MEMBRANE PROTEIN
Biological speciesEscherichia coli (E. coli)
Methodsubtomogram averaging / cryo EM / Resolution: 12.5 Å
AuthorsQin Z / Zhang P
Funding support United Kingdom, United States, European Union, 6 items
OrganizationGrant numberCountry
Wellcome Trust203141/Z/16/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BBSRC: B5R00550 B500.01 United Kingdom
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P50AI150481 United States
Wellcome Trust206422/Z/17/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S003339/1 United Kingdom
European Research Council (ERC)101021133European Union
CitationJournal: mBio / Year: 2023
Title: Structure of the native chemotaxis core signaling unit from phage E-protein lysed cells.
Authors: C Keith Cassidy / Zhuan Qin / Thomas Frosio / Khoosheh Gosink / Zhengyi Yang / Mark S P Sansom / Phillip J Stansfeld / John S Parkinson / Peijun Zhang /
Abstract: Bacterial chemotaxis is a ubiquitous behavior that enables cell movement toward or away from specific chemicals. It serves as an important model for understanding cell sensory signal transduction and ...Bacterial chemotaxis is a ubiquitous behavior that enables cell movement toward or away from specific chemicals. It serves as an important model for understanding cell sensory signal transduction and motility. Characterization of the molecular mechanisms underlying chemotaxis is of fundamental interest and requires a high-resolution structural picture of the sensing machinery, the chemosensory array. In this study, we combine cryo-electron tomography and molecular simulation to present the complete structure of the core signaling unit, the basic building block of chemosensory arrays, from . Our results provide new insight into previously poorly-resolved regions of the complex and offer a structural basis for designing new experiments to test mechanistic hypotheses.
History
DepositionAug 23, 2022-
Header (metadata) releaseFeb 8, 2023-
Map releaseFeb 8, 2023-
UpdateJul 31, 2024-
Current statusJul 31, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_15643.png

Downloads & links

-
Map

FileDownload / File: emd_15643.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNative Chemotaxis Core Signalling Complex in E. coli, focused alignment on the ligand binding domain, cubic map, unfiltered, unmasked
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.75 Å/pix.
x 192 pix.
= 527.04 Å		2.75 Å/pix.
x 192 pix.
= 527.04 Å		2.75 Å/pix.
x 192 pix.
= 527.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.745 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.24258539 - 0.32722747
Average (Standard dev.)0.000000000011791 (±0.028017946)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-96-96-96
Dimensions192192192
Spacing192192192
CellA=B=C: 527.04 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: half map. Native Chemotaxis Core Signalling Complex in...

Fileemd_15643_half_map_1.map
Annotationhalf map. Native Chemotaxis Core Signalling Complex in E. coli, focused alignment on the ligand binding domain, cubic map, unfiltered, unmasked
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map. Native Chemotaxis Core Signalling Complex in...

Fileemd_15643_half_map_2.map
Annotationhalf map. Native Chemotaxis Core Signalling Complex in E. coli, focused alignment on the ligand binding domain, cubic map, unfiltered, unmasked
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Native Chemotaxis Core Signalling Complex

EntireName: Native Chemotaxis Core Signalling Complex
Components
  • Complex: Native Chemotaxis Core Signalling Complex

-
Supramolecule #1: Native Chemotaxis Core Signalling Complex

SupramoleculeName: Native Chemotaxis Core Signalling Complex / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

-
Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 12.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 5100
ExtractionNumber tomograms: 33 / Number images used: 20000
Final angle assignmentType: OTHER / Software - Name: PROTOMO (ver. 0.9)

+
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