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- EMDB-6320: Structure of bacterial chemotaxis signaling CheA2-hexamer core co... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-6320 | |||||||||
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Title | Structure of bacterial chemotaxis signaling CheA2-hexamer core complex by cryo-electron tomography and subvolume averaging | |||||||||
![]() | Structure of bacterial chemotaxis signaling CheA2-hexamer core complex by cryo-electron tomography and subvolume averaging | |||||||||
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![]() | Bacterial chemotaxis / Signal transduction / cryo-Electron Tomography / Molecular dynamics simulation / all-atom | |||||||||
Function / homology | ![]() negative regulation of protein modification process / detection of chemical stimulus / methyl accepting chemotaxis protein complex / positive regulation of post-translational protein modification / protein histidine kinase binding / bacterial-type flagellum-dependent swimming motility / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / cell tip / 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 / protein histidine kinase binding / bacterial-type flagellum-dependent swimming motility / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / cell tip / protein histidine kinase activity / regulation of chemotaxis / thermotaxis / signal complex assembly / histidine kinase / phosphorelay sensor kinase activity / phosphorelay signal transduction system / cellular response to amino acid stimulus / establishment of localization in cell / protein homooligomerization / transmembrane signaling receptor activity / chemotaxis / protein domain specific binding / signal transduction / protein homodimerization activity / ATP binding / identical protein binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 17.5 Å | |||||||||
![]() | Cassidy CK / Himes BA / Alvarez FJ / Ma J / Zhou G / Perilla JR / Schulten K / Zhang P | |||||||||
![]() | ![]() Title: CryoEM and computer simulations reveal a novel kinase conformational switch in bacterial chemotaxis signaling. Authors: C Keith Cassidy / Benjamin A Himes / Frances J Alvarez / Jun Ma / Gongpu Zhao / Juan R Perilla / Klaus Schulten / Peijun Zhang / ![]() Abstract: Chemotactic responses in bacteria require large, highly ordered arrays of sensory proteins to mediate the signal transduction that ultimately controls cell motility. A mechanistic understanding of ...Chemotactic responses in bacteria require large, highly ordered arrays of sensory proteins to mediate the signal transduction that ultimately controls cell motility. A mechanistic understanding of the molecular events underlying signaling, however, has been hampered by the lack of a high-resolution structural description of the extended array. Here, we report a novel reconstitution of the array, involving the receptor signaling domain, histidine kinase CheA, and adaptor protein CheW, as well as a density map of the core-signaling unit at 11.3 Å resolution, obtained by cryo-electron tomography and sub-tomogram averaging. Extracting key structural constraints from our density map, we computationally construct and refine an atomic model of the core array structure, exposing novel interfaces between the component proteins. Using all-atom molecular dynamics simulations, we further reveal a distinctive conformational change in CheA. Mutagenesis and chemical cross-linking experiments confirm the importance of the conformational dynamics of CheA for chemotactic function. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 3.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.4 KB 13.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 3.8 KB | Display | ![]() |
Images | ![]() | 354.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Structure of bacterial chemotaxis signaling CheA2-hexamer core complex by cryo-electron tomography and subvolume averaging | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.01 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : tarCF CheA CheW
Entire | Name: tarCF CheA CheW |
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Components |
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-Supramolecule #1000: tarCF CheA CheW
Supramolecule | Name: tarCF CheA CheW / type: sample / ID: 1000 Oligomeric state: Hexamer of (CheA dimer, dimer of tarCF trimers of dimers, 2 CheW subunits) Number unique components: 3 |
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Molecular weight | Theoretical: 3.32 MDa |
-Macromolecule #1: Chemotaxis protein CheA
Macromolecule | Name: Chemotaxis protein CheA / type: protein_or_peptide / ID: 1 / Name.synonym: Bacterial Chemotaxis Histidine Kinase CheA / Number of copies: 12 / Oligomeric state: Dimer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 71.384 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | UniProtKB: Chemotaxis protein CheA |
-Macromolecule #2: Chemotaxis protein CheW
Macromolecule | Name: Chemotaxis protein CheW / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Oligomeric state: monomeric / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 18.083 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | UniProtKB: Chemotaxis protein CheW |
-Macromolecule #3: Methyl-accepting chemotaxis protein II
Macromolecule | Name: Methyl-accepting chemotaxis protein II / type: protein_or_peptide / ID: 3 / Name.synonym: tarCF Details: Cytoplasmic fragment of wild-type aspartate receptor Number of copies: 6 / Oligomeric state: trimer of dimers / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 31.209 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | UniProtKB: Methyl-accepting chemotaxis protein II |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | subtomogram averaging |
Aggregation state | 2D array |
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Sample preparation
Buffer | pH: 7.4 / Details: 75 mM Tris-HCl, 100 mM KCl, 5 mM MgCl2 |
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Grid | Details: Perforated R2/2 Quantifoil grids precoated with 10 nm fiducial gold beads on the backside of the grid |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER Method: Single-sided blotting to avoid disruption of the monolayer |
Details | Pseudo-crystalline 2D monolayer reconstituted on a lipid monolayer |
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Electron microscopy
Microscope | FEI POLARA 300 |
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Date | Jan 7, 2009 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 60 / Average electron dose: 60 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 49834 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 8.0 µm / Nominal defocus min: 4.0 µm / Nominal magnification: 39000 |
Sample stage | Specimen holder model: OTHER / Tilt series - Axis1 - Min angle: -70 ° / Tilt series - Axis1 - Max angle: 70 ° |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT |