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- EMDB-24425: Circular tandem repeat protein with novel repeat topology and enh... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-24425 | |||||||||
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Title | Circular tandem repeat protein with novel repeat topology and enhanced subunit contact surfaces | |||||||||
![]() | low resolution cryoEM map of cTRP trimers | |||||||||
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Biological species | unidentified (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.5 Å | |||||||||
![]() | Shen BW / Stoddard BL | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Design of functionalised circular tandem repeat proteins with longer repeat topologies and enhanced subunit contact surfaces. Authors: Jazmine P Hallinan / Lindsey A Doyle / Betty W Shen / Mesfin M Gewe / Brittany Takushi / Madison A Kennedy / Della Friend / James M Roberts / Philip Bradley / Barry L Stoddard / ![]() Abstract: Circular tandem repeat proteins ('cTRPs') are de novo designed protein scaffolds (in this and prior studies, based on antiparallel two-helix bundles) that contain repeated protein sequences and ...Circular tandem repeat proteins ('cTRPs') are de novo designed protein scaffolds (in this and prior studies, based on antiparallel two-helix bundles) that contain repeated protein sequences and structural motifs and form closed circular structures. They can display significant stability and solubility, a wide range of sizes, and are useful as protein display particles for biotechnology applications. However, cTRPs also demonstrate inefficient self-assembly from smaller subunits. In this study, we describe a new generation of cTRPs, with longer repeats and increased interaction surfaces, which enhanced the self-assembly of two significantly different sizes of homotrimeric constructs. Finally, we demonstrated functionalization of these constructs with (1) a hexameric array of peptide-binding SH2 domains, and (2) a trimeric array of anti-SARS CoV-2 VHH domains. The latter proved capable of sub-nanomolar binding affinities towards the viral receptor binding domain and potent viral neutralization function. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 31.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.5 KB 14.5 KB | Display Display | ![]() |
Images | ![]() | 92 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 350.5 KB | Display | ![]() |
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Full document | ![]() | 350 KB | Display | |
Data in XML | ![]() | 6.3 KB | Display | |
Data in CIF | ![]() | 7.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7rdrMC ![]() 6xr1C ![]() 6xr2C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | low resolution cryoEM map of cTRP trimers | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.16 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : trimer of tendon repeat protein
Entire | Name: trimer of tendon repeat protein |
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Components |
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-Supramolecule #1: trimer of tendon repeat protein
Supramolecule | Name: trimer of tendon repeat protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: circular tendon repeats based on de in silico structure design |
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Source (natural) | Organism: unidentified (others) |
Recombinant expression | Organism: ![]() ![]() |
Molecular weight | Theoretical: 150 KDa |
-Macromolecule #1: Circular tendon repeat protein
Macromolecule | Name: Circular tendon repeat protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: unidentified (others) |
Molecular weight | Theoretical: 53.141402 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: SELAARCLII LFQQLVELAR LAIESGDEEL LRRVSEWLEE VIKDMRRVVE QALREGNSEL AARILIILFQ QLVELARLAI ESGDEELLR RVSEWLEEVI KDMRRVVEQA LREGNSELAA RILIILFQQL VELARLAIES GDEELLRRVS EWLEEVIKDM R RVVEQALR ...String: SELAARCLII LFQQLVELAR LAIESGDEEL LRRVSEWLEE VIKDMRRVVE QALREGNSEL AARILIILFQ QLVELARLAI ESGDEELLR RVSEWLEEVI KDMRRVVEQA LREGNSELAA RILIILFQQL VELARLAIES GDEELLRRVS EWLEEVIKDM R RVVEQALR EGNSELAARI LIILFQQLVE LARLAIESGD EELLRRVSEW LEEVIKDMRR VVEQALREGN SELAARILII LF QQLVELA RLAIESGDEE LLRRVSEWLE EVIKDMRRVV EQALREGNSE LAARILIILF QQLVELARLA IESGDEELLR RVS EWLEEV IKDMRRVVEQ ALREGNSELA ARILIILFQQ LVELARLAIE SGDEELLRRV SEWLEEVIKD MRRVVEQALR EGNS ELACR ILIILFQQLV ELARLAIESG DEELLRRVSE WLEEVIKDMR RVVEQALREG N |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.4 mg/mL | |||||||||
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Buffer | pH: 7.5 Component:
Details: solution was diluted immediate prior to flash freezing | |||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 5 seconds before plunging. | |||||||||
Details | This sample was more disperse |
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Electron microscopy
Microscope | FEI TECNAI 20 |
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Temperature | Min: 100.0 K / Max: 100.0 K |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 1-50 / Number grids imaged: 1 / Number real images: 420 / Average exposure time: 10.0 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus min: 1.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 38000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | ![]() PDB-7rdr: |