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Yorodumi- EMDB-32788: SARS-CoV-2 Omicron variant spike RBD in complex with Fab XGv286 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32788 | |||||||||
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Title | SARS-CoV-2 Omicron variant spike RBD in complex with Fab XGv286 | |||||||||
Map data | ||||||||||
Sample |
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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 / membrane fusion / receptor-mediated endocytosis of virus by host cell / 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 | Homo sapiens (human) / Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
Authors | Wang X / Fu W | |||||||||
Funding support | 1 items
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Citation | Journal: Cell Res / Year: 2022 Title: Selection and structural bases of potent broadly neutralizing antibodies from 3-dose vaccinees that are highly effective against diverse SARS-CoV-2 variants, including Omicron sublineages. Authors: Lei Wang / Wangjun Fu / Linlin Bao / Zijing Jia / Yuxia Zhang / Yunjiao Zhou / Wei Wu / Jianbo Wu / Qianqian Zhang / Yidan Gao / Kang Wang / Qiao Wang / Chuan Qin / Xiangxi Wang / | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32788.map.gz | 166 MB | EMDB map data format | |
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Header (meta data) | emd-32788-v30.xml emd-32788.xml | 12.6 KB 12.6 KB | Display Display | EMDB header |
Images | emd_32788.png | 49.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32788 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32788 | HTTPS FTP |
-Validation report
Summary document | emd_32788_validation.pdf.gz | 442.3 KB | Display | EMDB validaton report |
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Full document | emd_32788_full_validation.pdf.gz | 441.9 KB | Display | |
Data in XML | emd_32788_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | emd_32788_validation.cif.gz | 7.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32788 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32788 | HTTPS FTP |
-Related structure data
Related structure data | 7wtjMC 7wtfC 7wtgC 7wthC 7wtiC 7wtkC 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_32788.map.gz / Format: CCP4 / Size: 178 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: 1.07 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : SARS-CoV-2 Omicron variant spike RBD in complex with Fab XGv286
Entire | Name: SARS-CoV-2 Omicron variant spike RBD in complex with Fab XGv286 |
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Components |
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-Supramolecule #1: SARS-CoV-2 Omicron variant spike RBD in complex with Fab XGv286
Supramolecule | Name: SARS-CoV-2 Omicron variant spike RBD in complex with Fab XGv286 type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #2: Fab XGv286
Supramolecule | Name: Fab XGv286 / type: complex / Chimera: Yes / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Supramolecule #3: SARS-CoV-2 Omicron variant spike RBD
Supramolecule | Name: SARS-CoV-2 Omicron variant spike RBD / type: complex / Chimera: Yes / ID: 3 / Parent: 1 / Macromolecule list: #3 |
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-Macromolecule #1: Heavy chain of XGv286
Macromolecule | Name: Heavy chain of XGv286 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 12.878352 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: VQLVQSGAEV KKPGASVKVS CKASGYTFSS YYIHWVRQAP GQGPEWMAII NPGDGGASYA QKFQGRVTLT RDTSTSTLYM ELSSLRSED TAVYYCARAE GSSWLGWFDP WGQGTLVTV |
-Macromolecule #2: Light chain of XGv286
Macromolecule | Name: Light chain of XGv286 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 11.43744 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: SVLTQPPSAS GTPGQRVTIS CSGSSSNIGS NYVYWYQQLP GTAPKLLIYR NNQRPSGVPD RFSGSRSGTS ASLAISGLRS EDEADYYCA AWDDGLSGSG WVFGGGTKLT |
-Macromolecule #3: Spike protein S1
Macromolecule | Name: Spike protein S1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 22.836854 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: PNITNLCPFD EVFNATRFAS VYAWNRKRIS NCVADYSVLY NLAPFFTFKC YGVSPTKLND LCFTNVYADS FVIRGDEVRQ IAPGQTGNI ADYNYKLPDD FTGCVIAWNS NKLDSKVSGN YNYLYRLFRK SNLKPFERDI STEIYQAGNK PCNGVAGFNC Y FPLRSYSF ...String: PNITNLCPFD EVFNATRFAS VYAWNRKRIS NCVADYSVLY NLAPFFTFKC YGVSPTKLND LCFTNVYADS FVIRGDEVRQ IAPGQTGNI ADYNYKLPDD FTGCVIAWNS NKLDSKVSGN YNYLYRLFRK SNLKPFERDI STEIYQAGNK PCNGVAGFNC Y FPLRSYSF RPTYGVGHQP YRVVVLSFEL LHAPATVCGP KKS |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN |
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Image recording | Film or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 60.0 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: 1.8 µm / Nominal defocus min: 1.2 µm |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 339195 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |