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- EMDB-27658: cryoEM map of de novo hallucinated homooligomer of C15-C5 symmetr... -
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Open data
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Basic information
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Title | cryoEM map of de novo hallucinated homooligomer of C15-C5 symmetry, design HALC15-5_262. | ||||||||||||
![]() | EM map of C15/C5 symmetric hallucinated protein oligomer assembly (HALC15-5_262). | ||||||||||||
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![]() | De novo protein design / Computational protein design / Machine learning / Hallucination / homo-oligomers / DE NOVO PROTEIN | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.69 Å | ||||||||||||
![]() | Wicky BIM / Milles LF / Courbet AC / Baker D | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Hallucinating symmetric protein assemblies. Authors: B I M Wicky / L F Milles / A Courbet / R J Ragotte / J Dauparas / E Kinfu / S Tipps / R D Kibler / M Baek / F DiMaio / X Li / L Carter / A Kang / H Nguyen / A K Bera / D Baker / ![]() Abstract: Deep learning generative approaches provide an opportunity to broadly explore protein structure space beyond the sequences and structures of natural proteins. Here, we use deep network hallucination ...Deep learning generative approaches provide an opportunity to broadly explore protein structure space beyond the sequences and structures of natural proteins. Here, we use deep network hallucination to generate a wide range of symmetric protein homo-oligomers given only a specification of the number of protomers and the protomer length. Crystal structures of seven designs are very similar to the computational models (median root mean square deviation: 0.6 angstroms), as are three cryo-electron microscopy structures of giant 10-nanometer rings with up to 1550 residues and symmetry; all differ considerably from previously solved structures. Our results highlight the rich diversity of new protein structures that can be generated using deep learning and pave the way for the design of increasingly complex components for nanomachines and biomaterials. #1: ![]() Title: Hallucinating protein assemblies Authors: Wicky BIM / Milles LF / Courbet A / Baker D | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 97.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.5 KB 16.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.9 KB | Display | ![]() |
Images | ![]() | 16.9 KB | ||
Masks | ![]() | 103 MB | ![]() | |
Filedesc metadata | ![]() | 4.9 KB | ||
Others | ![]() ![]() | 95.5 MB 95.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 719.9 KB | Display | ![]() |
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Full document | ![]() | 719.5 KB | Display | |
Data in XML | ![]() | 17.6 KB | Display | |
Data in CIF | ![]() | 22.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | EM map of C15/C5 symmetric hallucinated protein oligomer assembly (HALC15-5_262). | ||||||||||||||||||||
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
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: half map A of C15/C5 symmetric hallucinated protein...
File | emd_27658_half_map_1.map | ||||||||||||
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Annotation | half map A of C15/C5 symmetric hallucinated protein oligomer assembly (HALC15-5_262). | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map B of C15/C5 symmetric hallucinated protein...
File | emd_27658_half_map_2.map | ||||||||||||
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Annotation | half map B of C15/C5 symmetric hallucinated protein oligomer assembly (HALC15-5_262). | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : De novo hallucinated homooligomer of C15-C5 symmetry, design HALC...
Entire | Name: De novo hallucinated homooligomer of C15-C5 symmetry, design HALC15-5_262. |
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Components |
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-Supramolecule #1: De novo hallucinated homooligomer of C15-C5 symmetry, design HALC...
Supramolecule | Name: De novo hallucinated homooligomer of C15-C5 symmetry, design HALC15-5_262. type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: HALC15-5_262
Macromolecule | Name: HALC15-5_262 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: Expression vector pET-mod (others) |
Sequence | String: DVPLTDPKNL NEFLYALGEG LKGMKNLKKL TLTFPSNPLT IPGDISEGFR ELGEGLKGMK NLEELTVTFN DVPLTDPKN LNEFLYALGE GLKGMKNLKK LTLTFPSNPL TIPGDISEGF RELGEGLKGM KNLEELTVTF N DVPLTDPK NLNEFLYALG EGLKGMKNLK ...String: DVPLTDPKNL NEFLYALGEG LKGMKNLKKL TLTFPSNPLT IPGDISEGFR ELGEGLKGMK NLEELTVTFN DVPLTDPKN LNEFLYALGE GLKGMKNLKK LTLTFPSNPL TIPGDISEGF RELGEGLKGM KNLEELTVTF N DVPLTDPK NLNEFLYALG EGLKGMKNLK KLTLTFPSNP LTIPGDISEG FRELGEGLKG MKNLEELTVT FN |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 10 mg/mL | |||||||||
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Buffer | pH: 8.4 Component:
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Grid | Model: C-flat-2/2 | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III |
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Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |