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Open data
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Basic information
Entry | Database: PDB / ID: 9dnd | |||||||||||||||||||||||||||||||||||||||
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Title | Pseudosymmetric protein nanocage GI4 -F7 (local refinement) | |||||||||||||||||||||||||||||||||||||||
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![]() | VIRAL PROTEIN / Fusion protein / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / pseudosymmetric protein nanocages | |||||||||||||||||||||||||||||||||||||||
Biological species | synthetic construct (others) | |||||||||||||||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||||||||||||||||||||||||||||||||
![]() | Park, Y.J. / Dowling, Q.M. / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / King, N.P. / Veesler, D. | |||||||||||||||||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Hierarchical design of pseudosymmetric protein nanocages. Authors: Quinton M Dowling / Young-Jun Park / Chelsea N Fries / Neil C Gerstenmaier / Sebastian Ols / Erin C Yang / Adam J Wargacki / Annie Dosey / Yang Hsia / Rashmi Ravichandran / Carl D Walkey / ...Authors: Quinton M Dowling / Young-Jun Park / Chelsea N Fries / Neil C Gerstenmaier / Sebastian Ols / Erin C Yang / Adam J Wargacki / Annie Dosey / Yang Hsia / Rashmi Ravichandran / Carl D Walkey / Anika L Burrell / David Veesler / David Baker / Neil P King / ![]() Abstract: Discrete protein assemblies ranging from hundreds of kilodaltons to hundreds of megadaltons in size are a ubiquitous feature of biological systems and perform highly specialized functions. Despite ...Discrete protein assemblies ranging from hundreds of kilodaltons to hundreds of megadaltons in size are a ubiquitous feature of biological systems and perform highly specialized functions. Despite remarkable recent progress in accurately designing new self-assembling proteins, the size and complexity of these assemblies has been limited by a reliance on strict symmetry. Here, inspired by the pseudosymmetry observed in bacterial microcompartments and viral capsids, we developed a hierarchical computational method for designing large pseudosymmetric self-assembling protein nanomaterials. We computationally designed pseudosymmetric heterooligomeric components and used them to create discrete, cage-like protein assemblies with icosahedral symmetry containing 240, 540 and 960 subunits. At 49, 71 and 96 nm diameter, these nanocages are the largest bounded computationally designed protein assemblies generated to date. More broadly, by moving beyond strict symmetry, our work substantially broadens the variety of self-assembling protein architectures that are accessible through design. | |||||||||||||||||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 149.6 KB | Display | ![]() |
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PDB format | ![]() | 113.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 43.7 KB | Display | |
Data in CIF | ![]() | 61 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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: 24330.975 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() #2: Protein | | Mass: 23530.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() #3: Protein | | Mass: 22115.564 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Pseudosymmetric protein nanocages: GI4-F7 nanocage / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: synthetic construct (others) |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 8 |
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: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 60 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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 984020 / Symmetry type: POINT |