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Yorodumi- PDB-7wp8: Cryo-EM structure of SARS-CoV-2 recombinant spike protein STFK162... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wp8 | ||||||
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Title | Cryo-EM structure of SARS-CoV-2 recombinant spike protein STFK1628x in complex with three neutralizing antibodies | ||||||
Components |
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Keywords | IMMUNE SYSTEM/VIRAL PROTEIN / SARS-CoV-2 / spike / vaccine / neutralizing antibody / Cryo-EM / VIRAL PROTEIN / IMMUNE SYSTEM-VIRAL PROTEIN 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 / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / 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 Mus musculus (house mouse) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.88 Å | ||||||
Authors | Zheng, Q. / Sun, H. / Yuan, Q. / Li, S. / Xia, N. | ||||||
Funding support | 1items
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Citation | Journal: Cell Host Microbe / Year: 2022 Title: Lineage-mosaic and mutation-patched spike proteins for broad-spectrum COVID-19 vaccine. Authors: Yangtao Wu / Shaojuan Wang / Yali Zhang / Lunzhi Yuan / Qingbing Zheng / Min Wei / Yang Shi / Zikang Wang / Jian Ma / Kai Wang / Meifeng Nie / Jin Xiao / Zehong Huang / Peiwen Chen / Huilin ...Authors: Yangtao Wu / Shaojuan Wang / Yali Zhang / Lunzhi Yuan / Qingbing Zheng / Min Wei / Yang Shi / Zikang Wang / Jian Ma / Kai Wang / Meifeng Nie / Jin Xiao / Zehong Huang / Peiwen Chen / Huilin Guo / Miaolin Lan / Jingjing Xu / Wangheng Hou / Yunda Hong / Dabing Chen / Hui Sun / Hualong Xiong / Ming Zhou / Che Liu / Wenjie Guo / Huiyu Guo / Jiahua Gao / Congling Gan / Zhixiong Li / Haitao Zhang / Xinrui Wang / Shaowei Li / Tong Cheng / Qinjian Zhao / Yixin Chen / Ting Wu / Tianying Zhang / Jun Zhang / Hua Cao / Huachen Zhu / Quan Yuan / Yi Guan / Ningshao Xia / Abstract: SARS-CoV-2 spread in humans results in continuous emergence of new variants, highlighting the need for vaccines with broad-spectrum antigenic coverage. Using inter-lineage chimera and mutation-patch ...SARS-CoV-2 spread in humans results in continuous emergence of new variants, highlighting the need for vaccines with broad-spectrum antigenic coverage. Using inter-lineage chimera and mutation-patch strategies, we engineered a recombinant monomeric spike variant (STFK1628x) that contains key regions and residues across multiple SAR-CoV-2 variants. STFK1628x demonstrated high immunogenicity and mutually complementary antigenicity to its prototypic form (STFK). In hamsters, a bivalent vaccine composed of STFK and STFK1628x elicited high titers of broad-spectrum neutralizing antibodies to 19 circulating SARS-CoV-2 variants, including Omicron sublineages BA.1, BA.1.1, BA.2, BA.2.12.1, BA.2.75, and BA.4/5. Furthermore, this vaccine conferred robust protection against intranasal challenges by either SARS-CoV-2 ancestral strain or immune-evasive Beta and Omicron BA.1. Strikingly, vaccination with the bivalent vaccine in hamsters effectively blocked within-cage virus transmission of ancestral SARS-CoV-2, Beta variant, and Omicron BA.1 to unvaccinated sentinels. Thus, our study provided insight and antigen candidates for the development of next-generation COVID-19 vaccines. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wp8.cif.gz | 164.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wp8.ent.gz | 127.2 KB | Display | PDB format |
PDBx/mmJSON format | 7wp8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wp8_validation.pdf.gz | 964.6 KB | Display | wwPDB validaton report |
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Full document | 7wp8_full_validation.pdf.gz | 974.7 KB | Display | |
Data in XML | 7wp8_validation.xml.gz | 31.3 KB | Display | |
Data in CIF | 7wp8_validation.cif.gz | 46.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wp/7wp8 ftp://data.pdbj.org/pub/pdb/validation_reports/wp/7wp8 | HTTPS FTP |
-Related structure data
Related structure data | 32678MC 7wp6C 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 , 1 types, 1 molecules F
#4: Protein | Mass: 20803.342 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 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P0DTC2 |
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-Antibody , 6 types, 6 molecules CDEGHL
#1: Antibody | Mass: 11428.608 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
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#2: Antibody | Mass: 13027.506 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
#3: Antibody | Mass: 13681.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
#5: Antibody | Mass: 12449.835 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
#6: Antibody | Mass: 13159.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
#7: Antibody | Mass: 11278.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
-Sugars , 2 types, 2 molecules
#8: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#9: Sugar | ChemComp-NAG / |
-Details
Has ligand of interest | Y |
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-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) | Organism: Cricetulus griseus (Chinese hamster) | ||||||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F30 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.14_3259: / Classification: refinement |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 3.88 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 115589 / Symmetry type: POINT |