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Yorodumi- PDB-7cyh: Binding interface of SARS-CoV-2 RBD and its neutralizing antibody HB27 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7cyh | ||||||
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Title | Binding interface of SARS-CoV-2 RBD and its neutralizing antibody HB27 | ||||||
Components |
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Keywords | VIRAL PROTEIN / SARS-CoV-2 / Spike trimer / Neutralizing antibody | ||||||
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 / 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 | ELECTRON MICROSCOPY / 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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7cyh.cif.gz | 91.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cyh.ent.gz | 67.5 KB | Display | PDB format |
PDBx/mmJSON format | 7cyh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7cyh_validation.pdf.gz | 830.2 KB | Display | wwPDB validaton report |
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Full document | 7cyh_full_validation.pdf.gz | 843.7 KB | Display | |
Data in XML | 7cyh_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | 7cyh_validation.cif.gz | 29.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/7cyh ftp://data.pdbj.org/pub/pdb/validation_reports/cy/7cyh | HTTPS FTP |
-Related structure data
Related structure data | 30500MC 7cypC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 21772.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P0DTC2 |
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#2: Antibody | Mass: 11921.329 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human) |
#3: Antibody | Mass: 12917.422 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human) |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 8 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.10.1_2155: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 393321 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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