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Yorodumi- EMDB-40074: Cryo-EM map of synthetic cage_T3_5 reconstructed with T symmetry -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40074 | |||||||||
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Title | Cryo-EM map of synthetic cage_T3_5 reconstructed with T symmetry | |||||||||
Map data | cage_T3_5 refined with T symmetry | |||||||||
Sample |
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Keywords | synthetic / self-assembling / DE NOVO PROTEIN | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Coudray N / Redler R / Huddy TF / Hsia Y / Baker D / Ekiert D / Bhabha G | |||||||||
Funding support | United States, 1 items
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Citation | Journal: bioRxiv / Year: 2023 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 | emd_40074.map.gz | 86.5 MB | EMDB map data format | |
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Header (meta data) | emd-40074-v30.xml emd-40074.xml | 25 KB 25 KB | Display Display | EMDB header |
Images | emd_40074.png | 95.5 KB | ||
Filedesc metadata | emd-40074.cif.gz | 6.1 KB | ||
Others | emd_40074_additional_1.map.gz emd_40074_half_map_1.map.gz emd_40074_half_map_2.map.gz | 167.9 MB 165.4 MB 165.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40074 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40074 | HTTPS FTP |
-Validation report
Summary document | emd_40074_validation.pdf.gz | 783.1 KB | Display | EMDB validaton report |
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Full document | emd_40074_full_validation.pdf.gz | 782.7 KB | Display | |
Data in XML | emd_40074_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | emd_40074_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40074 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40074 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_40074.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | cage_T3_5 refined with T symmetry | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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
-Additional map: cage T3 5 refined with T symmetry (sharpened)
File | emd_40074_additional_1.map | ||||||||||||
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Annotation | cage_T3_5 refined with T symmetry (sharpened) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: cage T3 5 refined with T symmetry, half map A
File | emd_40074_half_map_1.map | ||||||||||||
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Annotation | cage_T3_5 refined with T symmetry, half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: cage T3 5 refined with T symmetry, half map B
File | emd_40074_half_map_2.map | ||||||||||||
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Annotation | cage_T3_5 refined with T symmetry, half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Expandable de novo designed complex cage_T3_5
Entire | Name: Expandable de novo designed complex cage_T3_5 |
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Components |
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-Supramolecule #1: Expandable de novo designed complex cage_T3_5
Supramolecule | Name: Expandable de novo designed complex cage_T3_5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: synthetic construct (others) |
-Macromolecule #1: cage_T3_5
Macromolecule | Name: cage_T3_5 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: mGSVELLAVA ALQELNIELA RALLEAVARL QELNIDLVRK TSELTDEKTI REEIRKVKEE SKRIVEEAEE LIRLAKLASE AIARMAEVAA RGAPPEELIK RLEELLKKAQ EAGMSPEIIH LLLELALAIV EARGVPPEQL AEFAERLVEI LREAGGSPEL VFELLRRIME ...String: mGSVELLAVA ALQELNIELA RALLEAVARL QELNIDLVRK TSELTDEKTI REEIRKVKEE SKRIVEEAEE LIRLAKLASE AIARMAEVAA RGAPPEELIK RLEELLKKAQ EAGMSPEIIH LLLELALAIV EARGVPPEQL AEFAERLVEI LREAGGSPEL VFELLRRIME IIARRGAPPE LLIELLERLL ELAREAGLSP RQIYLLLMLA LIIVYQRGVP PEQLAEFAEK LKEILREAGG SPELQKALKE LIEAIEELRG AGGSlehhhh hh |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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 |
-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: 1 / Number real images: 5854 / Average exposure time: 2.0 sec. / Average electron dose: 58.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
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 |
+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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