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Open data
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Basic information
Entry | ![]() | ||||||||||||
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Title | Dimer of SARS-CoV-2 S1 in complex with H18 and R1-32 Fabs | ||||||||||||
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![]() | Spike protein / RBD / Antibody / Fab / Viral protein / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||||||||
Function / homology | ![]() 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 | ![]() ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.66 Å | ||||||||||||
![]() | Yan Q / Gao X / Liu B / Hou R / He P / Li Z / Chen Q / Wang J / He J / Chen L ...Yan Q / Gao X / Liu B / Hou R / He P / Li Z / Chen Q / Wang J / He J / Chen L / Zhao J / Xiong X | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein helping to drive the genesis of Omicron variants Authors: Yan Q / Gao X / Liu B / Hou R / He P / Ma Y / Zhang Y / Zhang Y / Li Z / Chen Q / Wang J / Huang X / Liang H / Zheng H / Yao Y / Chen X / Niu X / He J / Chen L / Zhao J / Xiong X | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 48.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 22.9 KB 22.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.5 KB | Display | ![]() |
Images | ![]() | 84.7 KB | ||
Filedesc metadata | ![]() | 6.9 KB | ||
Others | ![]() ![]() | 48.8 MB 48.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8zhpMC ![]() 8zhdC ![]() 8zheC ![]() 8zhfC ![]() 8zhgC ![]() 8zhhC ![]() 8zhiC ![]() 8zhjC ![]() 8zhkC ![]() 8zhlC ![]() 8zhmC ![]() 8zhnC ![]() 8zhoC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.395 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_60111_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_60111_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Dimer of SARS-CoV-2 S1 in complex with H18 and R1-32 Fabs
+Supramolecule #1: Dimer of SARS-CoV-2 S1 in complex with H18 and R1-32 Fabs
+Supramolecule #2: SARS-CoV-2 S1
+Supramolecule #3: H18 Fab
+Supramolecule #4: R1-32 Fab
+Macromolecule #1: Spike glycoprotein
+Macromolecule #2: Heavy chain of R1-32 Fab
+Macromolecule #3: Light chain of R1-32 Fab
+Macromolecule #4: Light chain of H18 Fab
+Macromolecule #5: Heavy chain of H18 Fab
+Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 130000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |