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- PDB-8uja: T33-fn10 - Designed Tetrahedral Protein Cage Using Fragment-based... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8uja | ||||||
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Title | T33-fn10 - Designed Tetrahedral Protein Cage Using Fragment-based Hydrogen Bond Networks | ||||||
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![]() | DE NOVO PROTEIN / tetrahedral nanoparticle / designed protein / de novo interface / two-component complex / Rosetta | ||||||
Function / homology | Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / ClpP/crotonase-like domain superfamily / isomerase activity / Enoyl-CoA hydratase/isomerase![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Meador, K. / Sawaya, M.R. / Yeates, T.O. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A suite of designed protein cages using machine learning and protein fragment-based protocols. Authors: Kyle Meador / Roger Castells-Graells / Roman Aguirre / Michael R Sawaya / Mark A Arbing / Trent Sherman / Chethaka Senarathne / Todd O Yeates / ![]() Abstract: Designed protein cages and related materials provide unique opportunities for applications in biotechnology and medicine, but their creation remains challenging. Here, we apply computational ...Designed protein cages and related materials provide unique opportunities for applications in biotechnology and medicine, but their creation remains challenging. Here, we apply computational approaches to design a suite of tetrahedrally symmetric, self-assembling protein cages. For the generation of docked conformations, we emphasize a protein fragment-based approach, while for sequence design of the de novo interface, a comparison of knowledge-based and machine learning protocols highlights the power and increased experimental success achieved using ProteinMPNN. An analysis of design outcomes provides insights for improving interface design protocols, including prioritizing fragment-based motifs, balancing interface hydrophobicity and polarity, and identifying preferred polar contact patterns. In all, we report five structures for seven protein cages, along with two structures of intermediate assemblies, with the highest resolution reaching 2.0 Å using cryo-EM. This set of designed cages adds substantially to the body of available protein nanoparticles, and to methodologies for their creation. #1: ![]() Title: A Suite of Designed Protein Cages Using Machine Learning Algorithms and Protein Fragment-Based Protocols Authors: Meador, K. / Castells-Graells, R. / Aguirre, R. / Sawaya, M.R. / Arbing, M.A. / Sherman, T. / Senarathne, C. / Yeates, T.O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | 931.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 478.1 KB | Display | ![]() |
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Full document | ![]() | 492.7 KB | Display | |
Data in XML | ![]() | 52 KB | Display | |
Data in CIF | ![]() | 72.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8uf0C ![]() 8ui2C ![]() 8ukmC ![]() 8umpC ![]() 8umrC ![]() 8un1C 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 12122.230 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() #2: Protein | Mass: 27671.732 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: Saro_3457 / Production host: ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.09 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM HEPES pH 7.5, 10% PEG 8000, 10% Ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 1, 2022 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 6→92.11 Å / Num. obs: 18590 / % possible obs: 100 % / Redundancy: 10.6 % / Biso Wilson estimate: 356.46 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.174 / Rrim(I) all: 0.182 / Net I/σ(I): 9.17 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 400.92 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 6→92.11 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 80.4415769715 Å / Origin y: 45.1882430276 Å / Origin z: 43.114529597 Å
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Refinement TLS group | Selection details: all |