+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37241 | |||||||||
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Title | The interface structure of Omicron RBD binding to 5817 Fab | |||||||||
Map data | ||||||||||
Sample |
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Keywords | SARS-CoV-2 / Omicron / RBD / Fab / VIRAL PROTEIN | |||||||||
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 / 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) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Cao L / Wang X | |||||||||
Funding support | 1 items
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Citation | Journal: Cell Rep / Year: 2024 Title: Identification of a broad sarbecovirus neutralizing antibody targeting a conserved epitope on the receptor-binding domain. Authors: Yanqun Wang / Zhaoyong Zhang / Minnan Yang / Xinyi Xiong / Qihong Yan / Lei Cao / Peilan Wei / Yuting Zhang / Lu Zhang / Kexin Lv / Jiantao Chen / Xuesong Liu / Xiaochu Zhao / Juxue Xiao / ...Authors: Yanqun Wang / Zhaoyong Zhang / Minnan Yang / Xinyi Xiong / Qihong Yan / Lei Cao / Peilan Wei / Yuting Zhang / Lu Zhang / Kexin Lv / Jiantao Chen / Xuesong Liu / Xiaochu Zhao / Juxue Xiao / Shengnan Zhang / Airu Zhu / Mian Gan / Jingjun Zhang / Ruoxi Cai / Jianfen Zhuo / Yanjun Zhang / Haiyue Rao / Bin Qu / Yuanyuan Zhang / Lei Chen / Jun Dai / Linling Cheng / Qingtao Hu / Yaoqing Chen / Huibin Lv / Ray T Y So / Malik Peiris / Jingxian Zhao / Xiaoqing Liu / Chris Ka Pun Mok / Xiangxi Wang / Jincun Zhao / Abstract: Omicron, as the emerging variant with enhanced vaccine tolerance, has sharply disrupted most therapeutic antibodies. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) belongs to the ...Omicron, as the emerging variant with enhanced vaccine tolerance, has sharply disrupted most therapeutic antibodies. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) belongs to the subgenus Sarbecovirus, members of which share high sequence similarity. Herein, we report one sarbecovirus antibody, 5817, which has broad-spectrum neutralization capacity against SARS-CoV-2 variants of concern (VOCs) and SARS-CoV, as well as related bat and pangolin viruses. 5817 can hardly compete with six classes of receptor-binding-domain-targeted antibodies grouped by structural classifications. No obvious impairment in the potency is detected against SARS-CoV-2 Omicron and subvariants. The cryoelectron microscopy (cryo-EM) structure of neutralizing antibody 5817 in complex with Omicron spike reveals a highly conserved epitope, only existing at the receptor-binding domain (RBD) open state. Prophylactic and therapeutic administration of 5817 potently protects mice from SARS-CoV-2 Beta, Delta, Omicron, and SARS-CoV infection. This study reveals a highly conserved cryptic epitope targeted by a broad sarbecovirus neutralizing antibody, which would be beneficial to meet the potential threat of pre-emergent SARS-CoV-2 VOCs. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_37241.map.gz | 167.9 MB | EMDB map data format | |
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Header (meta data) | emd-37241-v30.xml emd-37241.xml | 17.1 KB 17.1 KB | Display Display | EMDB header |
Images | emd_37241.png | 24.2 KB | ||
Filedesc metadata | emd-37241.cif.gz | 5.6 KB | ||
Others | emd_37241_half_map_1.map.gz emd_37241_half_map_2.map.gz | 165.2 MB 165.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37241 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37241 | HTTPS FTP |
-Validation report
Summary document | emd_37241_validation.pdf.gz | 710.9 KB | Display | EMDB validaton report |
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Full document | emd_37241_full_validation.pdf.gz | 710.4 KB | Display | |
Data in XML | emd_37241_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | emd_37241_validation.cif.gz | 17.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37241 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37241 | HTTPS FTP |
-Related structure data
Related structure data | 8khdMC 8khcC 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_37241.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_37241_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_37241_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : The interface structure of Omicron RBD binding to 5817 Fab
Entire | Name: The interface structure of Omicron RBD binding to 5817 Fab |
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Components |
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-Supramolecule #1: The interface structure of Omicron RBD binding to 5817 Fab
Supramolecule | Name: The interface structure of Omicron RBD binding to 5817 Fab type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Macromolecule #1: Heavy chain of 5817
Macromolecule | Name: Heavy chain of 5817 / 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: 13.387045 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EVQLVESGGG LVKPGGSLRL SCAASGFSFS DAWMSWVRQA PGKGLEWVGR VSSEIGGGTT DYAAPVKGRF TISRDDSKNT LFLQMSSLK TEDTAVYYCT TGVDIVVMMY ADDAFDIWGQ GTMVTV |
-Macromolecule #2: Light chain of 5817
Macromolecule | Name: Light chain of 5817 / 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: 11.470526 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: ELTQDPAVSV ALGQTVRITC QGDSLRSYYA SWYQQKPGQA PVLVIYGKNN RPSGIPDRFS GSSSGNTASL TITGPQAEDE ADYYCTSRD SSGNHVIFGG GTKLTVLGQ |
-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: Severe acute respiratory syndrome coronavirus 2 |
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 UniProtKB: Spike glycoprotein |
-Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 1 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 5129 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |