+Open data
-Basic information
Entry | Database: PDB / ID: 6s1k | |||||||||
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Title | E. coli Core Signaling Unit, carrying QQQQ receptor mutation | |||||||||
Components |
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Keywords | SIGNALING 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 / cell tip / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / protein histidine kinase activity ...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 / cell tip / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / protein histidine kinase activity / regulation of chemotaxis / thermotaxis / signal complex assembly / receptor clustering / histidine kinase / phosphorelay sensor kinase activity / phosphorelay signal transduction system / cell motility / establishment of localization in cell / cellular response to amino acid stimulus / chemotaxis / transmembrane signaling receptor activity / protein domain specific binding / phosphorylation / signal transduction / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli str. K-12 substr. MG1655star (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 8.38 Å | |||||||||
Authors | Cassidy, C.K. | |||||||||
Funding support | United Kingdom, United States, 2items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6s1k.cif.gz | 427.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6s1k.ent.gz | 321.7 KB | Display | PDB format |
PDBx/mmJSON format | 6s1k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s1/6s1k ftp://data.pdbj.org/pub/pdb/validation_reports/s1/6s1k | HTTPS FTP |
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-Related structure data
Related structure data | 10050MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | 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 | 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 | 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
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: 2D ARRAY / 3D reconstruction method: subtomogram averaging |
-Sample preparation
Component | Name: core signaling complex of bacterial chemotaxis / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Escherichia coli str. K-12 substr. MG1655star (bacteria) |
Source (recombinant) | Organism: Escherichia coli str. K-12 substr. MG1655star (bacteria) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / C2 aperture diameter: 100 µm |
Image recording | Electron dose: 1.3 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) |
-Processing
EM software | Name: MDFF / Category: model refinement / Details: implemented in NAMD |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Symmetry | Point symmetry: C2 (2 fold cyclic) |
3D reconstruction | Resolution: 8.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 91636 / Symmetry type: POINT |
EM volume selection | Num. of tomograms: 24 / Num. of volumes extracted: 91636 |
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: global correlation coefficeint Details: MDFF was used to flexible fit atomic models of E. coli chemosensory proteins |