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Yorodumi- PDB-8f53: Top-down design of protein architectures with reinforcement learning -
+Open data
-Basic information
Entry | Database: PDB / ID: 8f53 | ||||||
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Title | Top-down design of protein architectures with reinforcement learning | ||||||
Components | RC_I_2 | ||||||
Keywords | DE NOVO PROTEIN / nanoparticle / capsid / oligomer / de novo design / rosetta / reinforcement learning | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.93 Å | ||||||
Authors | Borst, A.J. / Baker, D. | ||||||
Funding support | United States, 1items
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Citation | Journal: Science / Year: 2023 Title: Top-down design of protein architectures with reinforcement learning. Authors: Isaac D Lutz / Shunzhi Wang / Christoffer Norn / Alexis Courbet / Andrew J Borst / Yan Ting Zhao / Annie Dosey / Longxing Cao / Jinwei Xu / Elizabeth M Leaf / Catherine Treichel / Patrisia ...Authors: Isaac D Lutz / Shunzhi Wang / Christoffer Norn / Alexis Courbet / Andrew J Borst / Yan Ting Zhao / Annie Dosey / Longxing Cao / Jinwei Xu / Elizabeth M Leaf / Catherine Treichel / Patrisia Litvicov / Zhe Li / Alexander D Goodson / Paula Rivera-Sánchez / Ana-Maria Bratovianu / Minkyung Baek / Neil P King / Hannele Ruohola-Baker / David Baker / Abstract: As a result of evolutionary selection, the subunits of naturally occurring protein assemblies often fit together with substantial shape complementarity to generate architectures optimal for function ...As a result of evolutionary selection, the subunits of naturally occurring protein assemblies often fit together with substantial shape complementarity to generate architectures optimal for function in a manner not achievable by current design approaches. We describe a "top-down" reinforcement learning-based design approach that solves this problem using Monte Carlo tree search to sample protein conformers in the context of an overall architecture and specified functional constraints. Cryo-electron microscopy structures of the designed disk-shaped nanopores and ultracompact icosahedra are very close to the computational models. The icosohedra enable very-high-density display of immunogens and signaling molecules, which potentiates vaccine response and angiogenesis induction. Our approach enables the top-down design of complex protein nanomaterials with desired system properties and demonstrates the power of reinforcement learning in protein design. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8f53.cif.gz | 998.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8f53.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8f53.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8f53_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8f53_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8f53_validation.xml.gz | 75 KB | Display | |
Data in CIF | 8f53_validation.cif.gz | 124.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/8f53 ftp://data.pdbj.org/pub/pdb/validation_reports/f5/8f53 | HTTPS FTP |
-Related structure data
Related structure data | 28859MC 8f4xC 8f54C C: citing same article (ref.) M: map data used to model this data |
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-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 5885.969 Da / Num. of mol.: 60 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
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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 |
-Sample preparation
Component | Name: RC_I_2 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid type: Quantifoil R2/2 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1700 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 61.5 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 897978 | ||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 325728 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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