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- EMDB-27660: cryoEM map of de novo hallucinated homooligomer of C33-C3 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 C33-C3 symmetry, design HALC33-3_343 | ||||||||||||
![]() | EM map | ||||||||||||
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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: 6.32 Å | ||||||||||||
![]() | Wicky BIM / Milles LF / Courbet A / 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 | ![]() | 62.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.4 KB 16.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.6 KB | Display | ![]() |
Images | ![]() | 15.6 KB | ||
Masks | ![]() | 67 MB | ![]() | |
Filedesc metadata | ![]() | 4.8 KB | ||
Others | ![]() ![]() | 61.8 MB 61.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 724.9 KB | Display | ![]() |
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Full document | ![]() | 724.5 KB | Display | |
Data in XML | ![]() | 16.9 KB | Display | |
Data in CIF | ![]() | 21.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | EM map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.122 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
File | emd_27660_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_27660_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : De novo hallucinated homooligomer of C33-C3 symmetry, design HALC...
Entire | Name: De novo hallucinated homooligomer of C33-C3 symmetry, design HALC33-3_343 |
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Components |
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-Supramolecule #1: De novo hallucinated homooligomer of C33-C3 symmetry, design HALC...
Supramolecule | Name: De novo hallucinated homooligomer of C33-C3 symmetry, design HALC33-3_343 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: HALC33-3_343
Macromolecule | Name: HALC33-3_343 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: PSNWPEVAKY FDLGKALKPI GEGLQNLKNL KHLDLSFSFS LELYPGLPSN WPEVAKYFDL GKALKPIGEG LQNLKNLKH LDLSFSFSLE LYPGLPSNWP EVAKYFDLGK ALKPIGEGLQ NLKNLKHLDL SFSFSLELYP G LPSNWPEV AKYFDLGKAL KPIGEGLQNL ...String: PSNWPEVAKY FDLGKALKPI GEGLQNLKNL KHLDLSFSFS LELYPGLPSN WPEVAKYFDL GKALKPIGEG LQNLKNLKH LDLSFSFSLE LYPGLPSNWP EVAKYFDLGK ALKPIGEGLQ NLKNLKHLDL SFSFSLELYP G LPSNWPEV AKYFDLGKAL KPIGEGLQNL KNLKHLDLSF SFSLELYPGL PSNWPEVAKY FDLGKALKPI GE GLQNLKN LKHLDLSFSF SLELYPGLPS NWPEVAKYFD LGKALKPIGE GLQNLKNLKH LDLSFSFSLE LYP GLPSNW PEVAKYFDLG KALKPIGEGL QNLKNLKHLD LSFSFSLELY PGLPSNWPEV AKYFDLGKAL KPIG EGLQN LKNLKHLDLS FSFSLELYPG LPSNWPEVAK YFDLGKALKP IGEGLQNLKN LKHLDLSFSF SLELY PGLP SNWPEVAKYF DLGKALKPIG EGLQNLKNLK HLDLSFSFSL ELYPGLPSNW PEVAKYFDLG KALKPI GEG LQNLKNLKHL DLSFSFSLEL YPGL |
-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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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 |