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Open data
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Basic information
Entry | Database: PDB / ID: 9dgh | ||||||
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Title | Focused region on azoRhuA-bCDRhuA co-assembled nanotubes | ||||||
![]() | Rhamnulose-1-phosphate aldolase | ||||||
![]() | LYASE / Assembly | ||||||
Function / homology | ![]() rhamnulose-1-phosphate aldolase / rhamnulose-1-phosphate aldolase activity / rhamnose catabolic process / pentose catabolic process / aldehyde-lyase activity / metal ion binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.03 Å | ||||||
![]() | Zhang, Z. / Sonani, R.R. / Wang, F. / Egelman, E.H. / Tezcan, F.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Design of light- and chemically responsive protein assemblies through host-guest interactions. Authors: Zhiyin Zhang / Huat T Chiang / Ying Xia / Nicole Avakyan / Ravi R Sonani / Fengbin Wang / Edward H Egelman / James J De Yoreo / Lilo D Pozzo / F Akif Tezcan / ![]() Abstract: Host-guest interactions have been widely used to build responsive materials and molecular machines owing to their inherently dynamic nature, interaction specificity, and responsiveness to diverse ...Host-guest interactions have been widely used to build responsive materials and molecular machines owing to their inherently dynamic nature, interaction specificity, and responsiveness to diverse stimuli. Here we have set out to exploit these advantages of host-guest chemistry in the design of dynamic protein assemblies, using a symmetric protein, RhuA, as a building block. We show that RhuA variant individually modified with β-cyclodextrin (βCD) (host) or azobenzene (guest) functionalities can specifically pair with each other to form highly ordered 1- and 2-D assemblies. Association and dissociation RhuA-RhuA assemblies can be controlled by UV and visible light as well as by small-molecule modulators of βCD-azobenzene interactions. Kinetics analyses reveal that RhuA-RhuA nanotubes assemble without a nucleation barrier, a highly unusual occurrence for helical supramolecular systems. Taken together, our findings provide a compelling example for achieving complex structural and dynamic outcomes in protein assembly through simple chemical design. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 947.7 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 123.8 KB | Display | |
Data in CIF | ![]() | 189.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 46826MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | Mass: 30088.361 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P32169, rhamnulose-1-phosphate aldolase #2: Polysaccharide | Type: oligosaccharide / Mass: 1180.967 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: Chemical | ChemComp-ZN / #4: Chemical | Mass: 281.309 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H15N3O2 Has ligand of interest | Y | Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Helical assembly of azobenzene and beta-cyclodextrin modified RhuA Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2100 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 440307 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.61 Å2 | ||||||||||||||||||||||||
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