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Yorodumi- EMDB-16676: Delta-RBD complex with BA.2-07 fab, SARS1-34 fab and C1 nanobody -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16676 | |||||||||||||||
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Title | Delta-RBD complex with BA.2-07 fab, SARS1-34 fab and C1 nanobody | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Keywords | SARS-CoV2 / spike / glycoprotein / cornovavirus / antibody / fab / BA.4 / BA.5 / BA.2 / Delta variant / cross-protective / omicron variant / vaccine / therapeutic / complex / neutralising / convalescent sera / viral protein / immune system / C1 nanobody / SARS1-34 fab / BA.2-07 fab / VIRUS | |||||||||||||||
Function / homology | Function and homology information Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 / Homo sapiens (human) / Lama glama (llama) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||||||||
Authors | Duyvesteyn HME / Ren J / Stuart DI / Fry EE | |||||||||||||||
Funding support | United Kingdom, China, 4 items
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Citation | Journal: To Be Published Title: Potent cross-reactive mAbs from BA.4/5 breakthrough infection Authors: Duyvesteyn HME / Screaton G / Ren J / Stuart DI / Fry EE | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16676.map.gz | 122 MB | EMDB map data format | |
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Header (meta data) | emd-16676-v30.xml emd-16676.xml | 23.8 KB 23.8 KB | Display Display | EMDB header |
Images | emd_16676.png | 55.3 KB | ||
Filedesc metadata | emd-16676.cif.gz | 6.9 KB | ||
Others | emd_16676_half_map_1.map.gz emd_16676_half_map_2.map.gz | 226.9 MB 226.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16676 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16676 | HTTPS FTP |
-Validation report
Summary document | emd_16676_validation.pdf.gz | 717.9 KB | Display | EMDB validaton report |
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Full document | emd_16676_full_validation.pdf.gz | 717.5 KB | Display | |
Data in XML | emd_16676_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | emd_16676_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16676 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16676 | HTTPS FTP |
-Related structure data
Related structure data | 8ciiMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_16676.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.7303 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_16676_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_16676_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Delta-RBD complex with BA.2-07 fab, SARS1-34 fab and C1 nanobody
+Supramolecule #1: Delta-RBD complex with BA.2-07 fab, SARS1-34 fab and C1 nanobody
+Supramolecule #2: SARS1-34 fab
+Supramolecule #3: BA.2-07 fab
+Supramolecule #4: C1 nanobody
+Supramolecule #5: Delta-RBD
+Macromolecule #1: Spike protein S2'
+Macromolecule #2: SARS1-34 fab Heavy Chain
+Macromolecule #3: SARS1-34 fab Light Chain
+Macromolecule #4: BA.2-07 fab Heavy Chain
+Macromolecule #5: BA.2-07 fab Light Chain
+Macromolecule #6: C1 nanobody
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.5 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000 |
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
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 72 |
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Output model | PDB-8cii: |