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Yorodumi- EMDB-28858: Top-down design of protein architectures with reinforcement learning -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28858 | |||||||||
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Title | Top-down design of protein architectures with reinforcement learning | |||||||||
Map data | Sharpened Map | |||||||||
Sample |
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Keywords | nanoparticle / capsid / oligomer / de novo design / rosetta / cryoEM / DE NOVO PROTEIN / reinforcement learning | |||||||||
Biological species | Escherichia coli (E. coli) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.01 Å | |||||||||
Authors | Borst AJ / Baker D | |||||||||
Funding support | United States, 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28858.map.gz | 45.5 MB | EMDB map data format | |
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Header (meta data) | emd-28858-v30.xml emd-28858.xml | 17.5 KB 17.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28858_fsc.xml | 9.4 KB | Display | FSC data file |
Images | emd_28858.png | 118.6 KB | ||
Filedesc metadata | emd-28858.cif.gz | 5.3 KB | ||
Others | emd_28858_additional_1.map.gz emd_28858_half_map_1.map.gz emd_28858_half_map_2.map.gz | 45.5 MB 84.6 MB 84.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28858 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28858 | HTTPS FTP |
-Validation report
Summary document | emd_28858_validation.pdf.gz | 799.8 KB | Display | EMDB validaton report |
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Full document | emd_28858_full_validation.pdf.gz | 799.4 KB | Display | |
Data in XML | emd_28858_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | emd_28858_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28858 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28858 | HTTPS FTP |
-Related structure data
Related structure data | 8f4xMC 8f53C 8f54C M: atomic model generated by this map C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_28858.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened Map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.16 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Unsharpened Map
File | emd_28858_additional_1.map | ||||||||||||
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Annotation | Unsharpened Map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map A
File | emd_28858_half_map_1.map | ||||||||||||
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Annotation | Half Map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map B
File | emd_28858_half_map_2.map | ||||||||||||
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Annotation | Half Map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : RC_I_1-H11
Entire | Name: RC_I_1-H11 |
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Components |
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-Supramolecule #1: RC_I_1-H11
Supramolecule | Name: RC_I_1-H11 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: RC_I_1-H11
Macromolecule | Name: RC_I_1-H11 / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 7.764962 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MEEERRRHLA AAEARFLLEL GRPDEVLRLL ERLLEEGDPA LFAALRELLE SGDPLARLIA ETVFRRL |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.8 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R2/2 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Details: Thin layer of continuous carbon |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 59.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.8 µm |