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- PDB-6s1k: E. coli Core Signaling Unit, carrying QQQQ receptor mutation -

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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


: / 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 trimerization / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / 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 trimerization / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / protein histidine kinase activity / cell tip / thermotaxis / regulation of chemotaxis / signal complex assembly / receptor clustering / phosphorelay sensor kinase activity / histidine kinase / phosphorelay signal transduction system / cellular response to amino acid stimulus / cell motility / establishment of localization in cell / protein homooligomerization / chemotaxis / transmembrane signaling receptor activity / protein domain specific binding / 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-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 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

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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

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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

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Experimental details

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Experiment

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

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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

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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)

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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

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