[English] 日本語
Yorodumi
- PDB-8c5v: Chemotaxis core signalling unit from E protein lysed E. coli cells -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8c5v
TitleChemotaxis core signalling unit from E protein lysed E. coli cells
Components
  • (Chemotaxis protein CheA) x 2
  • Chemotaxis protein CheW
  • Methyl-accepting chemotaxis protein I
KeywordsMEMBRANE PROTEIN / Chemotaxis / Signal Transduction
Function / homology
Function and homology information


regulation of protein histidine kinase activity / negative regulation of protein modification process / detection of chemical stimulus / methyl accepting chemotaxis protein complex / positive regulation of post-translational protein modification / bacterial-type flagellum-dependent swimming motility / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / protein histidine kinase activity / cell tip ...regulation of protein histidine kinase activity / negative regulation of protein modification process / detection of chemical stimulus / methyl accepting chemotaxis protein complex / positive regulation of post-translational protein modification / bacterial-type flagellum-dependent swimming motility / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / protein histidine kinase activity / cell tip / regulation of chemotaxis / thermotaxis / signal complex assembly / histidine kinase / receptor clustering / phosphorelay signal transduction system / phosphorelay sensor kinase activity / establishment of localization in cell / cell motility / cellular response to amino acid stimulus / transmembrane signaling receptor activity / chemotaxis / protein domain specific binding / phosphorylation / signal transduction / ATP binding / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Chemotaxis protein CheW / CheY binding / CheY binding / Methyl-accepting chemotaxis protein, four helix bundle domain superfamily / Homologues of the ligand binding domain of Tar / Chemotaxis methyl-accepting receptor, methyl-accepting site / Bacterial chemotaxis sensory transducers signature. / Chemotaxis methyl-accepting receptor Tar-related, ligand-binding / Tar ligand binding domain homologue / Histidine kinase CheA-like, homodimeric domain ...Chemotaxis protein CheW / CheY binding / CheY binding / Methyl-accepting chemotaxis protein, four helix bundle domain superfamily / Homologues of the ligand binding domain of Tar / Chemotaxis methyl-accepting receptor, methyl-accepting site / Bacterial chemotaxis sensory transducers signature. / Chemotaxis methyl-accepting receptor Tar-related, ligand-binding / Tar ligand binding domain homologue / Histidine kinase CheA-like, homodimeric domain / CheY-binding domain of CheA / Histidine kinase CheA-like, homodimeric domain superfamily / Signal transducing histidine kinase, homodimeric domain / Signal transducing histidine kinase, homodimeric domain / CheW-like domain profile. / CheW-like domain / CheW-like domain superfamily / CheW-like domain / Two component signalling adaptor domain / Histidine Phosphotransfer domain / Chemotaxis methyl-accepting receptor / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
Methyl-accepting chemotaxis protein I / Chemotaxis protein CheA / Chemotaxis protein CheW
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 12 Å
AuthorsCassidy, C.K. / Qin, Z. / Zhang, P.
Funding support United Kingdom, United States, European Union, 6items
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
DepositionJan 10, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Structure summary / Category: audit_author
Revision 1.2Oct 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Nov 29, 2023Group: Database references / Category: citation / Item: _citation.journal_volume

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chemotaxis protein CheA
B: Chemotaxis protein CheA
C: Chemotaxis protein CheA
D: Chemotaxis protein CheA
E: Chemotaxis protein CheW
F: Chemotaxis protein CheW
G: Chemotaxis protein CheW
H: Chemotaxis protein CheW
I: Methyl-accepting chemotaxis protein I
J: Methyl-accepting chemotaxis protein I
K: Methyl-accepting chemotaxis protein I
L: Methyl-accepting chemotaxis protein I
M: Methyl-accepting chemotaxis protein I
N: Methyl-accepting chemotaxis protein I
O: Methyl-accepting chemotaxis protein I
P: Methyl-accepting chemotaxis protein I
Q: Methyl-accepting chemotaxis protein I
R: Methyl-accepting chemotaxis protein I
S: Methyl-accepting chemotaxis protein I
T: Methyl-accepting chemotaxis protein I


Theoretical massNumber of molelcules
Total (without water)844,12720
Polymers844,12720
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area135060 Å2
ΔGint-1181 kcal/mol
Surface area362030 Å2
MethodPISA

-
Components

#1: Protein Chemotaxis protein CheA


Mass: 42462.648 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P07363, histidine kinase
#2: Protein Chemotaxis protein CheA


Mass: 14874.573 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P07363, histidine kinase
#3: Protein
Chemotaxis protein CheW


Mass: 15675.938 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A964
#4: Protein
Methyl-accepting chemotaxis protein I / MCP-I / Serine chemoreceptor protein


Mass: 55562.367 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02942
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: subtomogram averaging

-
Sample preparation

ComponentName: Chemotaxis Core Signalling Unit from E-gene lysed E. coli cells.
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 3000 nm
Image recordingElectron dose: 3 e/Å2 / Avg electron dose per subtomogram: 100 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

-
Processing

EM software
IDNameVersionCategoryDetails
7NAMD2.14model fittingMDFF
10PROTOMO0.9final Euler assignment
13ISOLDE1.5model refinementChimeraX
CTF correctionDetails: emClarity / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5100 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 33 / Num. of volumes extracted: 20000
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL

+
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://pdbjlvh1.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