[English] 日本語
Yorodumi
- PDB-6s1k: E. coli Core Signaling Unit, carrying QQQQ receptor mutation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6s1k
TitleE. coli Core Signaling Unit, carrying QQQQ receptor mutation
Components
  • CheW
  • Chemotaxis protein CheA
  • Methyl-accepting chemotaxis protein I
KeywordsSIGNALING PROTEIN / chemotaxis / methyl-accepting chemotaxis protein / histidine kinase
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 / protein histidine kinase activity / protein trimerization / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis ...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 / protein histidine kinase activity / protein trimerization / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / cell tip / regulation of chemotaxis / thermotaxis / signal complex assembly / receptor clustering / histidine kinase / phosphorelay sensor kinase activity / phosphorelay signal transduction system / establishment of localization in cell / cellular response to amino acid stimulus / cell motility / protein homooligomerization / chemotaxis / transmembrane signaling receptor activity / protein domain specific binding / signal transduction / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm
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-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / 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 str. K-12 substr. MG1655star (bacteria)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 8.38 Å
AuthorsCassidy, C.K.
Funding support United Kingdom, United States, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/S003339/1 United Kingdom
National Science Foundation (United States)PHY1430124 United States
CitationJournal: Commun Biol / Year: 2020
Title: Structure and dynamics of the E. coli chemotaxis core signaling complex by cryo-electron tomography and molecular simulations.
Authors: C Keith Cassidy / Benjamin A Himes / Dapeng Sun / Jun Ma / Gongpu Zhao / John S Parkinson / Phillip J Stansfeld / Zaida Luthey-Schulten / Peijun Zhang /
Abstract: To enable the processing of chemical gradients, chemotactic bacteria possess large arrays of transmembrane chemoreceptors, the histidine kinase CheA, and the adaptor protein CheW, organized as ...To enable the processing of chemical gradients, chemotactic bacteria possess large arrays of transmembrane chemoreceptors, the histidine kinase CheA, and the adaptor protein CheW, organized as coupled core-signaling units (CSU). Despite decades of study, important questions surrounding the molecular mechanisms of sensory signal transduction remain unresolved, owing especially to the lack of a high-resolution CSU structure. Here, we use cryo-electron tomography and sub-tomogram averaging to determine a structure of the Escherichia coli CSU at sub-nanometer resolution. Based on our experimental data, we use molecular simulations to construct an atomistic model of the CSU, enabling a detailed characterization of CheA conformational dynamics in its native structural context. We identify multiple, distinct conformations of the critical P4 domain as well as asymmetries in the localization of the P3 bundle, offering several novel insights into the CheA signaling mechanism.
History
DepositionJun 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-10050
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-10050
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chemotaxis protein CheA
B: Chemotaxis protein CheA
C: CheW
D: CheW
E: Methyl-accepting chemotaxis protein I
F: Methyl-accepting chemotaxis protein I
G: Methyl-accepting chemotaxis protein I
H: Methyl-accepting chemotaxis protein I
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


Theoretical massNumber of molelcules
Total (without water)893,04916
Polymers893,04916
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area40110 Å2
ΔGint-369 kcal/mol
Surface area113410 Å2
MethodPISA

-
Components

#1: Protein Chemotaxis protein CheA


Mass: 71454.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655star (bacteria)
Gene: cheA, b1888, JW1877
Production host: Escherichia coli str. K-12 substr. MG1655star (bacteria)
References: UniProt: P07363, histidine kinase
#2: Protein CheW


Mass: 18095.693 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655star (bacteria)
Production host: Escherichia coli str. K-12 substr. MG1655star (bacteria)
References: UniProt: P0A964*PLUS
#3: Protein
Methyl-accepting chemotaxis protein I / MCP-I / Serine chemoreceptor protein


Mass: 59495.758 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655star (bacteria)
Gene: tsr, cheD, b4355, JW4318
Production host: Escherichia coli str. K-12 substr. MG1655star (bacteria)
References: UniProt: P02942

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: subtomogram averaging

-
Sample preparation

ComponentName: core signaling complex of bacterial chemotaxis / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli str. K-12 substr. MG1655star (bacteria)
Source (recombinant)Organism: Escherichia coli str. K-12 substr. MG1655star (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Cs: 2 mm / C2 aperture diameter: 100 µm
Image recordingElectron dose: 1.3 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)

-
Processing

EM softwareName: MDFF / Category: model refinement / Details: implemented in NAMD
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 8.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 91636 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 24 / Num. of volumes extracted: 91636
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: global correlation coefficeint
Details: MDFF was used to flexible fit atomic models of E. coli chemosensory proteins

+
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