|Entry||Database: EMDB / ID: EMD-20063|
|Title||Fractal-like assemblies of designed AtzA and AtzC proteins|
|Sample||Designed proteins AtzA-pY:AtzC-SH2Design|
|Biological species||Pseudomonas sp. (bacteria)|
|Method||electron tomography / cryo EM|
|Authors||Dai W / Chen M / Khare S|
|Citation||Journal: Nat Chem / Year: 2019|
Title: Stimulus-responsive self-assembly of protein-based fractals by computational design.
Authors: Nancy E Hernández / William A Hansen / Denzel Zhu / Maria E Shea / Marium Khalid / Viacheslav Manichev / Matthew Putnins / Muyuan Chen / Anthony G Dodge / Lu Yang / Ileana Marrero-Berríos / Melissa Banal / Phillip Rechani / Torgny Gustafsson / Leonard C Feldman / Sang-Hyuk Lee / Lawrence P Wackett / Wei Dai / Sagar D Khare /
Abstract: Fractal topologies, which are statistically self-similar over multiple length scales, are pervasive in nature. The recurrence of patterns in fractal-shaped branched objects, such as trees, lungs and ...Fractal topologies, which are statistically self-similar over multiple length scales, are pervasive in nature. The recurrence of patterns in fractal-shaped branched objects, such as trees, lungs and sponges, results in a high surface area to volume ratio, which provides key functional advantages including molecular trapping and exchange. Mimicking these topologies in designed protein-based assemblies could provide access to functional biomaterials. Here we describe a computational design approach for the reversible self-assembly of proteins into tunable supramolecular fractal-like topologies in response to phosphorylation. Guided by atomic-resolution models, we develop fusions of Src homology 2 (SH2) domain or a phosphorylatable SH2-binding peptide, respectively, to two symmetric, homo-oligomeric proteins. Mixing the two designed components resulted in a variety of dendritic, hyperbranched and sponge-like topologies that are phosphorylation-dependent and self-similar over three decades (~10 nm-10 μm) of length scale, in agreement with models from multiscale computational simulations. Designed assemblies perform efficient phosphorylation-dependent capture and release of cargo proteins.
|Date||Deposition: Apr 5, 2019 / Header (metadata) release: May 1, 2019 / Map release: Jul 10, 2019 / Update: Jul 10, 2019|
Downloads & links
|File||Download / File: emd_20063.map.gz / Format: CCP4 / Size: 17.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
generated in cubic-lattice coordinate
|Voxel size||X=Y=Z: 27.9 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire Designed proteins AtzA-pY:AtzC-SH2
|Entire||Name: Designed proteins AtzA-pY:AtzC-SH2Design / Number of components: 1|
-Component #1: protein, Designed proteins AtzA-pY:AtzC-SH2
|Protein||Name: Designed proteins AtzA-pY:AtzC-SH2Design / Recombinant expression: No|
|Source||Species: Pseudomonas sp. (bacteria)|
|Source (engineered)||Expression System: Escherichia coli (E. coli)|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||pH: 7|
|Vitrification||Instrument: LEICA EM GP / Cryogen name: ETHANE / Temperature: 293 K / Humidity: 90 %|
-Electron microscopy imaging
Model: Talos Arctica / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI ARCTICA|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 1 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 39000.0 X (nominal), 39000.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 4000.0 - 6000.0 nm / Energy filter: GIF Quantum LS|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: (93.0 - 110.0 K)|
|Camera||Detector: GATAN K2 QUANTUM (4k x 4k)|
|Processing||Method: electron tomography / Number of sections: 60|
|3D reconstruction||Algorithm: BACK PROJECTION / Software: EMAN2|
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