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Yorodumi- EMDB-30500: Binding interface of SARS-CoV-2 RBD and its neutralizing antibody HB27 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30500 | |||||||||
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Title | Binding interface of SARS-CoV-2 RBD and its neutralizing antibody HB27 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | SARS-CoV-2 / Spike trimer / Neutralizing antibody / 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 / 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 | Severe acute respiratory syndrome coronavirus 2 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Wang X / Zhu L | |||||||||
Citation | Journal: Natl Sci Rev / Year: 2021 Title: Double lock of a potent human therapeutic monoclonal antibody against SARS-CoV-2. Authors: Ling Zhu / Yong-Qiang Deng / Rong-Rong Zhang / Zhen Cui / Chun-Yun Sun / Chang-Fa Fan / Xiaorui Xing / Weijin Huang / Qi Chen / Na-Na Zhang / Qing Ye / Tian-Shu Cao / Nan Wang / Lei Wang / ...Authors: Ling Zhu / Yong-Qiang Deng / Rong-Rong Zhang / Zhen Cui / Chun-Yun Sun / Chang-Fa Fan / Xiaorui Xing / Weijin Huang / Qi Chen / Na-Na Zhang / Qing Ye / Tian-Shu Cao / Nan Wang / Lei Wang / Lei Cao / Huiyu Wang / Desheng Kong / Juan Ma / Chunxia Luo / Yanjing Zhang / Jianhui Nie / Yao Sun / Zhe Lv / Neil Shaw / Qianqian Li / Xiao-Feng Li / Junjie Hu / Liangzhi Xie / Zihe Rao / Youchun Wang / Xiangxi Wang / Cheng-Feng Qin / Abstract: Receptor recognition and subsequent membrane fusion are essential for the establishment of successful infection by SARS-CoV-2. Halting these steps can cure COVID-19. Here we have identified and ...Receptor recognition and subsequent membrane fusion are essential for the establishment of successful infection by SARS-CoV-2. Halting these steps can cure COVID-19. Here we have identified and characterized a potent human monoclonal antibody, HB27, that blocks SARS-CoV-2 attachment to its cellular receptor at sub-nM concentrations. Remarkably, HB27 can also prevent SARS-CoV-2 membrane fusion. Consequently, a single dose of HB27 conferred effective protection against SARS-CoV-2 in two established mouse models. Rhesus macaques showed no obvious adverse events when administrated with 10 times the effective dose of HB27. Cryo-EM studies on complex of SARS-CoV-2 trimeric S with HB27 Fab reveal that three Fab fragments work synergistically to occlude SARS-CoV-2 from binding to the ACE2 receptor. Binding of the antibody also restrains any further conformational changes of the receptor binding domain, possibly interfering with progression from the prefusion to the postfusion stage. These results suggest that HB27 is a promising candidate for immuno-therapies against COVID-19. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30500.map.gz | 28.6 MB | EMDB map data format | |
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Header (meta data) | emd-30500-v30.xml emd-30500.xml | 11 KB 11 KB | Display Display | EMDB header |
Images | emd_30500.png | 112.5 KB | ||
Filedesc metadata | emd-30500.cif.gz | 4.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30500 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30500 | HTTPS FTP |
-Validation report
Summary document | emd_30500_validation.pdf.gz | 485.6 KB | Display | EMDB validaton report |
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Full document | emd_30500_full_validation.pdf.gz | 485.2 KB | Display | |
Data in XML | emd_30500_validation.xml.gz | 5.8 KB | Display | |
Data in CIF | emd_30500_validation.cif.gz | 6.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30500 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30500 | HTTPS FTP |
-Related structure data
Related structure data | 7cyhMC 7cypC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_30500.map.gz / Format: CCP4 / Size: 30.5 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: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Complex of SARS-CoV-2 RBD and its neutralizing antibody HB27
Entire | Name: Complex of SARS-CoV-2 RBD and its neutralizing antibody HB27 |
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Components |
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-Supramolecule #1: Complex of SARS-CoV-2 RBD and its neutralizing antibody HB27
Supramolecule | Name: Complex of SARS-CoV-2 RBD and its neutralizing antibody HB27 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: SARS-CoV-2 RBD
Supramolecule | Name: SARS-CoV-2 RBD / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Supramolecule #3: HB27 antibody
Supramolecule | Name: HB27 antibody / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Macromolecule #1: Spike glycoprotein
Macromolecule | Name: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 21.772391 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: NLCPFGEVFN ATRFASVYAW NRKRISNCVA DYSVLYNSAS FSTFKCYGVS PTKLNDLCFT NVYADSFVIR GDEVRQIAPG QTGKIADYN YKLPDDFTGC VIAWNSNNLD SKVGGNYNYL YRLFRKSNLK PFERDISTEI YQAGSTPCNG VEGFNCYFPL Q SYGFQPTN ...String: NLCPFGEVFN ATRFASVYAW NRKRISNCVA DYSVLYNSAS FSTFKCYGVS PTKLNDLCFT NVYADSFVIR GDEVRQIAPG QTGKIADYN YKLPDDFTGC VIAWNSNNLD SKVGGNYNYL YRLFRKSNLK PFERDISTEI YQAGSTPCNG VEGFNCYFPL Q SYGFQPTN GVGYQPYRVV VLSFELLHAP ATVCGP UniProtKB: Spike glycoprotein |
-Macromolecule #2: Light chain of HB27
Macromolecule | Name: Light chain of HB27 / 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: 11.921329 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: IVLTQSPTLS LSPGERATLS CRASESVDNY GISFMNWFQQ KPGQAPRLLI YAASNQGSGI PSRFSGSGSG TDFSLTISSL EPEDFAVYF CQQSKEVPRI FGQGTKVEIL K |
-Macromolecule #3: Heavy chain of HB27
Macromolecule | Name: Heavy chain of HB27 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 12.917422 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: VKLVESGGGL VKPGGSLRLS CAASGFTFTN YGMSWVRQAP GKRLEWVAEI SSGGSYTYYP DTVTGRFTIS RDNAKNTLYL QMNSLRAED TAVYYCARFR YGGGGTVDYW GQGTLVTVSS |
-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 KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (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: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 393321 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |