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Open data
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Basic information
Entry | Database: PDB / ID: 7yvm | ||||||
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Title | Omicron BA.4/5 SARS-CoV-2 S RBD in complex with TH272 Fab | ||||||
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![]() | ANTIVIRAL PROTEIN/VIRAL PROTEIN / COVID-19 / spike glycoprotein / virus / VIRAL PROTEIN / ANTIVIRAL PROTEIN-VIRAL PROTEIN complex | ||||||
Function / homology | ![]() 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 / Attachment and Entry / membrane fusion / symbiont-mediated suppression of host innate immune response / 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 | ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
![]() | Guo, Y. / Zhang, G. / Liang, J. / Liu, F. / Rao, Z. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Discovery and characterization of potent pan-variant SARS-CoV-2 neutralizing antibodies from individuals with Omicron breakthrough infection. Authors: Yu Guo / Guangshun Zhang / Qi Yang / Xiaowei Xie / Yang Lu / Xuelian Cheng / Hui Wang / Jingxi Liang / Jielin Tang / Yuxin Gao / Hang Shang / Jun Dai / Yongxia Shi / Jiaxi Zhou / Jun Zhou / ...Authors: Yu Guo / Guangshun Zhang / Qi Yang / Xiaowei Xie / Yang Lu / Xuelian Cheng / Hui Wang / Jingxi Liang / Jielin Tang / Yuxin Gao / Hang Shang / Jun Dai / Yongxia Shi / Jiaxi Zhou / Jun Zhou / Hangtian Guo / Haitao Yang / Jianwei Qi / Lijun Liu / Shihui Ma / Biao Zhang / Qianyu Huo / Yi Xie / Junping Wu / Fang Dong / Song Zhang / Zhiyong Lou / Yan Gao / Zidan Song / Wenming Wang / Zixian Sun / Xiaoming Yang / Dongsheng Xiong / Fengjiang Liu / Xinwen Chen / Ping Zhu / Ximo Wang / Tao Cheng / Zihe Rao / ![]() Abstract: The SARS-CoV-2 Omicron variant evades most currently approved neutralizing antibodies (nAbs) and caused drastic decrease of plasma neutralizing activity elicited by vaccination or prior infection, ...The SARS-CoV-2 Omicron variant evades most currently approved neutralizing antibodies (nAbs) and caused drastic decrease of plasma neutralizing activity elicited by vaccination or prior infection, urging the need for the development of pan-variant antivirals. Breakthrough infection induces a hybrid immunological response with potentially broad, potent and durable protection against variants, therefore, convalescent plasma from breakthrough infection may provide a broadened repertoire for identifying elite nAbs. We performed single-cell RNA sequencing (scRNA-seq) and BCR sequencing (scBCR-seq) of B cells from BA.1 breakthrough-infected patients who received 2 or 3 previous doses of inactivated vaccine. Elite nAbs, mainly derived from the IGHV2-5 and IGHV3-66/53 germlines, showed potent neutralizing activity across Wuhan-Hu-1, Delta, Omicron sublineages BA.1 and BA.2 at picomolar NT values. Cryo-EM analysis revealed diverse modes of spike recognition and guides the design of cocktail therapy. A single injection of paired antibodies cocktail provided potent protection in the K18-hACE2 transgenic female mouse model of SARS-CoV-2 infection. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 104.5 KB | Display | ![]() |
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PDB format | ![]() | 68.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 34132MC ![]() 7yveC ![]() 7yvfC ![]() 7yvgC ![]() 7yvhC ![]() 7yviC ![]() 7yvjC ![]() 7yvkC ![]() 7yvlC ![]() 7yvnC ![]() 7yvoC ![]() 7yvpC ![]() 8gouC ![]() 8gpyC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Antibody | Mass: 11740.976 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Antibody | Mass: 12710.209 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Protein | Mass: 142592.938 Da / Num. of mol.: 1 / Mutation: K986P, V987P Source method: isolated from a genetically manipulated source Details: Omicron BA.5 Source: (gene. exp.) ![]() ![]() Gene: S, 2 / Production host: ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
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Buffer solution | pH: 7.4 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.16_3549: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 140520 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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