+Open data
-Basic information
Entry | Database: PDB / ID: 7wwm | |||||||||
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Title | S protein of Delta variant in complex with ZWC6 | |||||||||
Components |
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Keywords | VIRAL PROTEIN / SARS-CoV-2 | |||||||||
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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / 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 Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Guo, Y.Y. / Zhang, Y.Y. / Zhou, Q. | |||||||||
Funding support | China, 2items
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Citation | Journal: Signal Transduct Target Ther / Year: 2022 Title: Broadly neutralizing antibodies against Omicron-included SARS-CoV-2 variants induced by vaccination. Authors: Xiangyang Chi / Yingying Guo / Guanying Zhang / Hancong Sun / Jun Zhang / Min Li / Zhengshan Chen / Jin Han / Yuanyuan Zhang / Xinghai Zhang / Pengfei Fan / Zhe Zhang / Busen Wang / Xiaodong ...Authors: Xiangyang Chi / Yingying Guo / Guanying Zhang / Hancong Sun / Jun Zhang / Min Li / Zhengshan Chen / Jin Han / Yuanyuan Zhang / Xinghai Zhang / Pengfei Fan / Zhe Zhang / Busen Wang / Xiaodong Zai / Xuelian Han / Meng Hao / Ting Fang / Jinghan Xu / Shipo Wu / Yi Chen / Yingying Fang / Yunzhu Dong / Bingjie Sun / Jinlong Zhang / Jianmin Li / Guangyu Zhao / Changming Yu / Qiang Zhou / Wei Chen / Abstract: The SARS-CoV-2 Omicron variant shows substantial resistance to neutralization by infection- and vaccination-induced antibodies, highlighting the demands for research on the continuing discovery of ...The SARS-CoV-2 Omicron variant shows substantial resistance to neutralization by infection- and vaccination-induced antibodies, highlighting the demands for research on the continuing discovery of broadly neutralizing antibodies (bnAbs). Here, we developed a panel of bnAbs against Omicron and other variants of concern (VOCs) elicited by vaccination of adenovirus-vectored COVID-19 vaccine (Ad5-nCoV). We also investigated the human longitudinal antibody responses following vaccination and demonstrated how the bnAbs evolved over time. A monoclonal antibody (mAb), named ZWD12, exhibited potent and broad neutralization against SARS-CoV-2 variants Alpha, Beta, Gamma, Kappa, Delta, and Omicron by blocking the spike protein binding to the angiotensin-converting enzyme 2 (ACE2) and provided complete protection in the challenged prophylactic and therapeutic K18-hACE2 transgenic mouse model. We defined the ZWD12 epitope by determining its structure in complex with the spike (S) protein via cryo-electron microscopy. This study affords the potential to develop broadly therapeutic mAb drugs and suggests that the RBD epitope bound by ZWD12 is a rational target for the design of a broad spectrum of vaccines. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wwm.cif.gz | 668.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wwm.ent.gz | 551.4 KB | Display | PDB format |
PDBx/mmJSON format | 7wwm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wwm_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 7wwm_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 7wwm_validation.xml.gz | 90.3 KB | Display | |
Data in CIF | 7wwm_validation.cif.gz | 140.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ww/7wwm ftp://data.pdbj.org/pub/pdb/validation_reports/ww/7wwm | HTTPS FTP |
-Related structure data
Related structure data | 32871MC 7wwlC 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
#1: Protein | Mass: 141102.281 Da / Num. of mol.: 3 Mutation: Six proline substitutions at residues 817, 892, 899, 942, 986, and 987 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Variant: Delta / Production host: Homo sapiens (human) / References: UniProt: P0DTC2 #2: Antibody | Mass: 13463.000 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #3: Antibody | Mass: 11835.223 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: 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 #5: Sugar | ChemComp-NAG / 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
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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: 2200 nm / Nominal defocus min: 1200 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software | Name: cryoSPARC / Category: 3D reconstruction |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 137204 / Symmetry type: POINT |