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Yorodumi- EMDB-33125: Cryo-EM structure of Omicron RBD complexed with ACE2 and 304 Fab -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33125 | |||||||||
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Title | Cryo-EM structure of Omicron RBD complexed with ACE2 and 304 Fab | |||||||||
Map data | Main EP map | |||||||||
Sample |
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Function / homology | Function and homology information positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / regulation of systemic arterial blood pressure by renin-angiotensin / positive regulation of gap junction assembly / tryptophan transport / regulation of cardiac conduction / regulation of vasoconstriction ...positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / regulation of systemic arterial blood pressure by renin-angiotensin / positive regulation of gap junction assembly / tryptophan transport / regulation of cardiac conduction / regulation of vasoconstriction / peptidyl-dipeptidase activity / maternal process involved in female pregnancy / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / metallocarboxypeptidase activity / carboxypeptidase activity / negative regulation of signaling receptor activity / Attachment and Entry / positive regulation of cardiac muscle contraction / regulation of cytokine production / viral life cycle / blood vessel diameter maintenance / brush border membrane / negative regulation of smooth muscle cell proliferation / regulation of transmembrane transporter activity / cilium / negative regulation of ERK1 and ERK2 cascade / positive regulation of reactive oxygen species metabolic process / metallopeptidase activity / endocytic vesicle membrane / regulation of cell population proliferation / virus receptor activity / regulation of inflammatory response / endopeptidase activity / 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 / Potential therapeutics for SARS / 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 / symbiont entry into host cell / apical plasma membrane / membrane raft / endoplasmic reticulum lumen / 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 / cell surface / extracellular space / extracellular exosome / zinc ion binding / extracellular region / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.05 Å | |||||||||
Authors | Zhao Z / Qi J / Gao FG | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Omicron SARS-CoV-2 mutations stabilize spike up-RBD conformation and lead to a non-RBM-binding monoclonal antibody escape Authors: Zhao Z / Zhou J / Tian M / Huang M / Liu S / Xie Y / Han P / Bai C / Han P / Zheng A / Fu L / Gao Y / Peng Q / Li Y / Chai Y / Zhang Z / Zhao X / Song H / Qi J / Wang Q / Wang P / Gao GF | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33125.map.gz | 117.4 MB | EMDB map data format | |
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Header (meta data) | emd-33125-v30.xml emd-33125.xml | 21.4 KB 21.4 KB | Display Display | EMDB header |
Images | emd_33125.png | 62.8 KB | ||
Others | emd_33125_half_map_1.map.gz emd_33125_half_map_2.map.gz | 115.8 MB 115.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33125 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33125 | HTTPS FTP |
-Validation report
Summary document | emd_33125_validation.pdf.gz | 617 KB | Display | EMDB validaton report |
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Full document | emd_33125_full_validation.pdf.gz | 616.5 KB | Display | |
Data in XML | emd_33125_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | emd_33125_validation.cif.gz | 16.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33125 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33125 | HTTPS FTP |
-Related structure data
Related structure data | 7xcpMC 7xchC 7xciC 7xckC 7xcoC 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_33125.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Main EP map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.669 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half map A
File | emd_33125_half_map_1.map | ||||||||||||
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Annotation | half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map B
File | emd_33125_half_map_2.map | ||||||||||||
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Annotation | half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : CryoEM structure of Omicron RBD complexed with ACE2 and 304 Fab
+Supramolecule #1: CryoEM structure of Omicron RBD complexed with ACE2 and 304 Fab
+Supramolecule #2: ACE2
+Supramolecule #3: Omicron RBD
+Supramolecule #4: 304 Fab
+Macromolecule #1: Processed angiotensin-converting enzyme 2
+Macromolecule #2: Spike protein S1
+Macromolecule #3: Heavy chain of 304 Fab
+Macromolecule #4: Lignt chain of 304 Fab
+Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose
+Macromolecule #7: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Grid | Material: GRAPHENE OXIDE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % |
-Electron microscopy
Microscope | FEI/PHILIPS CM300FEG/T |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1635544 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |