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- EMDB-40076: Cryo-EM map of synthetic cage_T3_5+2 reconstructed without symmet... -
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Open data
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Basic information
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Title | Cryo-EM map of synthetic cage_T3_5+2 reconstructed without symmetry (C1) | |||||||||
![]() | cage_T3_5 2 refined without symmetry (C1) | |||||||||
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![]() | synthetic / self-assembling / DE NOVO PROTEIN | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.7 Å | |||||||||
![]() | Coudray N / Redler R / Huddy TF / Hsia Y / Baker D / Ekiert D / Bhabha G | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Blueprinting expandable nanomaterials with standardized protein building blocks. Abstract: A wooden house frame consists of many different lumber pieces, but because of the regularity of these building blocks, the structure can be designed using straightforward geometrical principles. The ...A wooden house frame consists of many different lumber pieces, but because of the regularity of these building blocks, the structure can be designed using straightforward geometrical principles. The design of multicomponent protein assemblies in comparison has been much more complex, largely due to the irregular shapes of protein structures . Here we describe extendable linear, curved, and angled protein building blocks, as well as inter-block interactions that conform to specified geometric standards; assemblies designed using these blocks inherit their extendability and regular interaction surfaces, enabling them to be expanded or contracted by varying the number of modules, and reinforced with secondary struts. Using X-ray crystallography and electron microscopy, we validate nanomaterial designs ranging from simple polygonal and circular oligomers that can be concentrically nested, up to large polyhedral nanocages and unbounded straight "train track" assemblies with reconfigurable sizes and geometries that can be readily blueprinted. Because of the complexity of protein structures and sequence-structure relationships, it has not been previously possible to build up large protein assemblies by deliberate placement of protein backbones onto a blank 3D canvas; the simplicity and geometric regularity of our design platform now enables construction of protein nanomaterials according to "back of an envelope" architectural blueprints. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 60.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 23.1 KB 23.1 KB | Display Display | ![]() |
Images | ![]() | 54.5 KB | ||
Masks | ![]() | 125 MB | ![]() | |
Filedesc metadata | ![]() | 6.1 KB | ||
Others | ![]() ![]() | 116 MB 116 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1006.5 KB | Display | ![]() |
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Full document | ![]() | 1006 KB | Display | |
Data in XML | ![]() | 14.2 KB | Display | |
Data in CIF | ![]() | 16.7 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 | cage_T3_5 2 refined without symmetry (C1) | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.8248 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: cage T3 5 2 refined without symmetry (C1), half map B
File | emd_40076_half_map_1.map | ||||||||||||
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Annotation | cage_T3_5 2 refined without symmetry (C1), half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: cage T3 5 2 refined without symmetry (C1), half map A
File | emd_40076_half_map_2.map | ||||||||||||
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Annotation | cage_T3_5 2 refined without symmetry (C1), half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Expandable de novo designed complex cage_T3_5+2
Entire | Name: Expandable de novo designed complex cage_T3_5+2 |
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Components |
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-Supramolecule #1: Expandable de novo designed complex cage_T3_5+2
Supramolecule | Name: Expandable de novo designed complex cage_T3_5+2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: synthetic construct (others) |
-Macromolecule #1: cage_T3_5+2
Macromolecule | Name: cage_T3_5+2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: mGSVELLAVA ALQELNIELA RALLEAVARL QELNIDLVRK TSELTDEKTI REEIRKVKEE SKRIVEEAEE LIRLAKLASE AIARMAEVAA RGAPPELLIE LLERLLKKAQ EAGMSPEIIH LLLELALAIV EARGVPPEQL AEFAERLVEI LREAGGSPEL VFELLARILE ...String: mGSVELLAVA ALQELNIELA RALLEAVARL QELNIDLVRK TSELTDEKTI REEIRKVKEE SKRIVEEAEE LIRLAKLASE AIARMAEVAA RGAPPELLIE LLERLLKKAQ EAGMSPEIIH LLLELALAIV EARGVPPEQL AEFAERLVEI LREAGGSPEL VFELLARILE IIERRGAPPE LLAELAERLV ELAREAGLSP ELVFELLRRA MEIVARRGAP PELLIELLER LLELAREAGL SPRQIYLLLM LALIIVYQRG VPPEQLAEFA EKLKEILREA GGSPELQKAL KELIEAIEEL RGAGGSGGSG GSlehhhhhh |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 5 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 30 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 3 / Number real images: 19358 / Average exposure time: 2.0 sec. / Average electron dose: 58.8 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: 2.2 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: Other / Chain - Initial model type: in silico model / Details: de novo designed model |
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