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- EMDB-15641: Structure of the Native Chemotaxis Core Signalling Complex from E... -

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Basic information

Entry
Database: EMDB / ID: EMD-15641
TitleStructure of the Native Chemotaxis Core Signalling Complex from E-gene lysed E. coli cells.
Map dataNative Chemotaxis Core Signalling Complex from E. coli using subtomo averaging, cubic map without filtering or masking
Sample
  • Complex: Native Chemotaxis Core Signalling Complex
    • Protein or peptide: Chemotaxis protein CheA
KeywordsChemotaxis Core Signalling Complex from E. coli / Chemotaxis / Signal Transduction / Chemoreceptor / Core signaling complex / MEMBRANE PROTEIN
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 / phosphorylation / 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, 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)
Methodsubtomogram averaging / cryo EM / Resolution: 12.0 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

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Structure visualization

Supplemental images

emd_15641.png

Downloads & links

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Map

FileDownload / File: emd_15641.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNative Chemotaxis Core Signalling Complex from E. coli using subtomo averaging, cubic map without filtering or masking
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: 0.09
Minimum - Maximum-0.2987305 - 0.46617848
Average (Standard dev.)-0.000000000004459 (±0.04120924)
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 °

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Supplemental data

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Half map: Native Chemotaxis Core Signalling Complex from E. coli...

Fileemd_15641_half_map_1.map
AnnotationNative Chemotaxis Core Signalling Complex from E. coli using subtomo averaging, cubic half map without filtering or masking
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Native Chemotaxis Core Signalling Complex from E. coli...

Fileemd_15641_half_map_2.map
AnnotationNative Chemotaxis Core Signalling Complex from E. coli using subtomo averaging, cubic half map without filtering or masking
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Native Chemotaxis Core Signalling Complex

EntireName: Native Chemotaxis Core Signalling Complex
Components
  • Complex: Native Chemotaxis Core Signalling Complex
    • Protein or peptide: Chemotaxis protein CheA

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Supramolecule #1: Native Chemotaxis Core Signalling Complex

SupramoleculeName: Native Chemotaxis Core Signalling Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Chemotaxis protein CheA

MacromoleculeName: Chemotaxis protein CheA / type: protein_or_peptide / ID: 1 / Details: E. coli histidine kinase CheA / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
SequenceString: MSMDISDFYQ TFFDEADELL ADMEQHLLVL QPEAPDAEQL NAIFRAAHSI KGGAGTFGFS VLQETTHLME NLLDEARRGE MQLNTDIINL FLETKDIMQE QLDAYKQSQE PDAASFDYIC QALRQLALEA KGETPSAVTR LSVVAKSEPQ DEQSRSQSPR RIILSRLKAG ...String:
MSMDISDFYQ TFFDEADELL ADMEQHLLVL QPEAPDAEQL NAIFRAAHSI KGGAGTFGFS VLQETTHLME NLLDEARRGE MQLNTDIINL FLETKDIMQE QLDAYKQSQE PDAASFDYIC QALRQLALEA KGETPSAVTR LSVVAKSEPQ DEQSRSQSPR RIILSRLKAG EVDLLEEELG HLTTLTDVVK GADSLSAILP GDIAEDDITA VLCFVIEADQ ITFETVEVSP KISTPPVLKL AAEQAPTGRV EREKTTRSNE STSIRVAVEK VDQLINLVGE LVITQSMLAQ RSSELDPVNH GDLITSMGQL QRNARDLQES VMSIRMMPME YVFSRYPRLV RDLAGKLGKQ VELTLVGSST ELDKSLIERI IDPLTHLVRN SLDHGIELPE KRLAAGKNSV GNLILSAEHQ GGNICIEVTD DGAGLNRERI LAKAASQGLT VSENMSDDEV AMLIFAPGFS TAEQVTDVSG RGVGMDVVKR NIQKMGGHVE IQSKQGTGTT IRILLPLTLA ILDGMSVRVA DEVFILPLNA VMESLQPREA DLHPLAGGER VLEVRGEYLP IVELWKVFNV AGAKTEATQG IVVILQSGGR RYALLVDQLI GQHQVVVKNL ESNYRKVPGI SAATILGDGS VALIVDVSAL QAINREQRMA NTAA

UniProtKB: Chemotaxis protein CheA

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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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

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Image processing

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 12.0 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)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8c5v:
Chemotaxis core signalling unit from E protein lysed E. coli cells

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