[English] 日本語
![](img/lk-miru.gif)
- EMDB-42390: T33-ml23 Assembly Intermediate - Designed Tetrahedral Protein Cag... -
+
Open data
-
Basic information
Entry | ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | T33-ml23 Assembly Intermediate - Designed Tetrahedral Protein Cage Using Machine Learning Algorithms | |||||||||
![]() | ||||||||||
![]() |
| |||||||||
![]() | Nanohedra / protein cage / tetrahedral / de novo protein interface / machine learning / two components / ProteinMPNN / nanoparticle / DE NOVO PROTEIN | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
![]() | Castells-Graells R / Meador K / Sawaya MR / Yeates TO | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() 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. | |||||||||
History |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 49.8 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 16 KB 16 KB | Display Display | ![]() |
Images | ![]() | 111.9 KB | ||
Filedesc metadata | ![]() | 5.6 KB | ||
Others | ![]() ![]() | 49 MB 49 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 940.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 940.5 KB | Display | |
Data in XML | ![]() | 11.7 KB | Display | |
Data in CIF | ![]() | 13.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8un1MC ![]() 8uf0C ![]() 8ui2C ![]() 8ujaC ![]() 8ukmC ![]() 8umpC ![]() 8umrC M: atomic model generated by this map C: citing same article ( |
---|
-
Links
EMDB pages | ![]() ![]() |
---|
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: #2
File | emd_42390_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_42390_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : T33-ml23 Assembly Intermediate - Designed Tetrahedral Protein Cag...
Entire | Name: T33-ml23 Assembly Intermediate - Designed Tetrahedral Protein Cage Using Machine Learning |
---|---|
Components |
|
-Supramolecule #1: T33-ml23 Assembly Intermediate - Designed Tetrahedral Protein Cag...
Supramolecule | Name: T33-ml23 Assembly Intermediate - Designed Tetrahedral Protein Cage Using Machine Learning type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 400 KDa |
-Macromolecule #1: T33-ml23-redesigned-CutA-fold
Macromolecule | Name: T33-ml23-redesigned-CutA-fold / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 11.231908 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MAIIETTTPT EEEAKAIAKK LLENRLIAEA IITPALTKIY RENGEIKSET VTRVTLYTEE ENVPKAVTYI KAIHPDPIPP IIVITPTDA NPAYKGWVAF ET |
-Macromolecule #2: T33-ml23-redesigned-tandem-BMC-T-fold
Macromolecule | Name: T33-ml23-redesigned-tandem-BMC-T-fold / type: protein_or_peptide / ID: 2 / Number of copies: 9 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 20.260586 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: DPERPALGIL ELSSYARGVK VADAALKAAP VKLLKCEPVE PGRALIMLLG EPEDVAKAMI AALDVAGLGS GNLIDYALIP EIHPQLLPF LKEYKKSEPI KDPNKAIIVA EVSTVAAAIE AADVALRLAN VELTSMRLAE HIGGRASFTL IGDKEDVEKA A RAIRGVAG ERLLDLEIIE KPVEALIGNE FF |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Concentration | 0.6 mg/mL |
---|---|
Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 1.16 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
-
Image processing
Startup model | Type of model: NONE |
---|---|
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 47115 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
---|---|
Output model | ![]() PDB-8un1: |