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Yorodumi- EMDB-36850: SARS-CoV-2 Omicron BA.1 spike protein in complex with a self-asse... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36850 | |||||||||
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Title | SARS-CoV-2 Omicron BA.1 spike protein in complex with a self-assembling trivalent nanobody Tr67 | |||||||||
Map data | SARS-CoV-2 Omicron BA.1 spike protein in complex with a self-assembling trivalent nanobody Tr67 | |||||||||
Sample |
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Keywords | trivalent nanobody / viral neutralization / Omicron BA.1 / 3-RBD-up conformation / VIRAL PROTEIN | |||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.0 Å | |||||||||
Authors | Jiang XY / Qin Q / Qian JQ / Zhu HX / Huang Q | |||||||||
Funding support | China, 2 items
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Citation | Journal: J Nanobiotechnology / Year: 2024 Title: Computational design and engineering of self-assembling multivalent microproteins with therapeutic potential against SARS-CoV-2. Authors: Qin Qin / Xinyi Jiang / Liyun Huo / Jiaqiang Qian / Hongyuan Yu / Haixia Zhu / Wenhao Du / Yuhui Cao / Xing Zhang / Qiang Huang / Abstract: Multivalent drugs targeting homo-oligomeric viral surface proteins, such as the SARS-CoV-2 trimeric spike (S) protein, have the potential to elicit more potent and broad-spectrum therapeutic ...Multivalent drugs targeting homo-oligomeric viral surface proteins, such as the SARS-CoV-2 trimeric spike (S) protein, have the potential to elicit more potent and broad-spectrum therapeutic responses than monovalent drugs by synergistically engaging multiple binding sites on viral targets. However, rational design and engineering of nanoscale multivalent protein drugs are still lacking. Here, we developed a computational approach to engineer self-assembling trivalent microproteins that simultaneously bind to the three receptor binding domains (RBDs) of the S protein. This approach involves four steps: structure-guided linker design, molecular simulation evaluation of self-assembly, experimental validation of self-assembly state, and functional testing. Using this approach, we first designed trivalent constructs of the microprotein miniACE2 (MP) with different trimerization scaffolds and linkers, and found that one of the constructs (MP-5ff) showed high trimerization efficiency, good conformational homogeneity, and strong antiviral neutralizing activity. With its trimerization unit (5ff), we then engineered a trivalent nanobody (Tr67) that exhibited potent and broad neutralizing activity against the dominant Omicron variants, including XBB.1 and XBB.1.5. Cryo-EM complex structure confirmed that Tr67 stably binds to all three RBDs of the Omicron S protein in a synergistic form, locking them in the "3-RBD-up" conformation that could block human receptor (ACE2) binding and potentially facilitate immune clearance. Therefore, our approach provides an effective strategy for engineering potent protein drugs against SARS-CoV-2 and other deadly coronaviruses. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36850.map.gz | 65 MB | EMDB map data format | |
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Header (meta data) | emd-36850-v30.xml emd-36850.xml | 19.5 KB 19.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_36850_fsc.xml | 10 KB | Display | FSC data file |
Images | emd_36850.png | 84.4 KB | ||
Filedesc metadata | emd-36850.cif.gz | 4.6 KB | ||
Others | emd_36850_additional_1.map.gz emd_36850_half_map_1.map.gz emd_36850_half_map_2.map.gz | 77.9 MB 65.2 MB 65.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36850 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36850 | HTTPS FTP |
-Validation report
Summary document | emd_36850_validation.pdf.gz | 625.7 KB | Display | EMDB validaton report |
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Full document | emd_36850_full_validation.pdf.gz | 625.3 KB | Display | |
Data in XML | emd_36850_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | emd_36850_validation.cif.gz | 22.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36850 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36850 | HTTPS FTP |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_36850.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | SARS-CoV-2 Omicron BA.1 spike protein in complex with a self-assembling trivalent nanobody Tr67 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.57 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: SARS-CoV-2 Omicron BA.1 spike protein in complex with...
File | emd_36850_additional_1.map | ||||||||||||
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Annotation | SARS-CoV-2 Omicron BA.1 spike protein in complex with a self-assembling trivalent nanobody Tr67 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_36850_half_map_1.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2
File | emd_36850_half_map_2.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SARS-CoV-2 Omicron BA.1 spike protein in complex with a self-asse...
Entire | Name: SARS-CoV-2 Omicron BA.1 spike protein in complex with a self-assembling trivalent nanobody Tr67 |
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Components |
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-Supramolecule #1: SARS-CoV-2 Omicron BA.1 spike protein in complex with a self-asse...
Supramolecule | Name: SARS-CoV-2 Omicron BA.1 spike protein in complex with a self-assembling trivalent nanobody Tr67 type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Supramolecule #2: Trivalent nanobody
Supramolecule | Name: Trivalent nanobody / type: complex / ID: 2 / Parent: 1 |
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Source (natural) | Organism: synthetic construct (others) |
-Supramolecule #3: SARS-CoV-2 Omicron BA.1 spike protein
Supramolecule | Name: SARS-CoV-2 Omicron BA.1 spike protein / type: complex / ID: 3 / Parent: 1 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | 3D array |
-Sample preparation
Concentration | 0.3 mg/mL | ||||||||||||
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Buffer | pH: 7.4 Component:
Details: 10 mM HEPES,150 mM NaCl,1% glycerol | ||||||||||||
Grid | Model: Quantifoil / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 296.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 43.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 92000 |