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Yorodumi- PDB-8h08: SARS-CoV-2 BA.1 variants S ectodomain trimer in complex with neut... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8h08 | ||||||
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Title | SARS-CoV-2 BA.1 variants S ectodomain trimer in complex with neutralizing antibody 10-5B and 6-2C | ||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 BA.1 / antibody / VIRUS / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Wang, X. / Wang, Z. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Inactivated vaccine-elicited potent antibodies can broadly neutralize SARS-CoV-2 circulating variants. Authors: Yubin Liu / Ziyi Wang / Xinyu Zhuang / Shengnan Zhang / Zhicheng Chen / Yan Zou / Jie Sheng / Tianpeng Li / Wanbo Tai / Jinfang Yu / Yanqun Wang / Zhaoyong Zhang / Yunfeng Chen / Liangqin ...Authors: Yubin Liu / Ziyi Wang / Xinyu Zhuang / Shengnan Zhang / Zhicheng Chen / Yan Zou / Jie Sheng / Tianpeng Li / Wanbo Tai / Jinfang Yu / Yanqun Wang / Zhaoyong Zhang / Yunfeng Chen / Liangqin Tong / Xi Yu / Linjuan Wu / Dong Chen / Renli Zhang / Ningyi Jin / Weijun Shen / Jincun Zhao / Mingyao Tian / Xinquan Wang / Gong Cheng / Abstract: A full understanding of the inactivated COVID-19 vaccine-mediated antibody responses to SARS-CoV-2 circulating variants will inform vaccine effectiveness and vaccination development strategies. Here, ...A full understanding of the inactivated COVID-19 vaccine-mediated antibody responses to SARS-CoV-2 circulating variants will inform vaccine effectiveness and vaccination development strategies. Here, we offer insights into the inactivated vaccine-induced antibody responses after prime-boost vaccination at both the polyclonal and monoclonal levels. We characterized the VDJ sequence of 118 monoclonal antibodies (mAbs) and found that 20 neutralizing mAbs showed varied potency and breadth against a range of variants including XBB.1.5, BQ.1.1, and BN.1. Bispecific antibodies (bsAbs) based on nonoverlapping mAbs exhibited enhanced neutralizing potency and breadth against the most antibody-evasive strains, such as XBB.1.5, BQ.1.1, and BN.1. The passive transfer of mAbs or their bsAb effectively protected female hACE2 transgenic mice from challenge with an infectious Delta or Omicron BA.2 variant. The neutralization mechanisms of these antibodies were determined by structural characterization. Overall, a broad spectrum of potent and distinct neutralizing antibodies can be induced in individuals immunized with the SARS-CoV-2 inactivated vaccine BBIBP-CorV, suggesting the application potential of inactivated vaccines and these antibodies for preventing infection by SARS-CoV-2 circulating variants. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8h08.cif.gz | 757.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8h08.ent.gz | 594.7 KB | Display | PDB format |
PDBx/mmJSON format | 8h08.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8h08_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8h08_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8h08_validation.xml.gz | 116.1 KB | Display | |
Data in CIF | 8h08_validation.cif.gz | 176.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h0/8h08 ftp://data.pdbj.org/pub/pdb/validation_reports/h0/8h08 | HTTPS FTP |
-Related structure data
Related structure data | 34411MC 7x2hC 7xd2C 8h07C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 2 types, 6 molecules ABCDFL
#1: Protein | Mass: 144416.078 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: BA.1 Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2 #2: Protein | Mass: 12517.014 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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-Antibody , 3 types, 9 molecules JHPNIQOKR
#3: Antibody | Mass: 11368.661 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #4: Antibody | Mass: 13723.151 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #5: Antibody | Mass: 11685.123 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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-Sugars , 1 types, 3 molecules
#6: Sugar |
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-Details
Has ligand of interest | Y |
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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
Component |
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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 / Nominal defocus max: 1500 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 372377 / Symmetry type: POINT |