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Yorodumi- PDB-7e3k: Ultrapotent SARS-CoV-2 neutralizing antibodies with protective ef... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7e3k | ||||||
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Title | Ultrapotent SARS-CoV-2 neutralizing antibodies with protective efficacy against newly emerged mutational variants | ||||||
Components |
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Keywords | VIRAL PROTEIN / COVID-19 / spike glycoprotein / virus / 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 | Guo, H. / Li, T. / Liu, F. / Gao, Y. / Ji, X. / Yang, H. | ||||||
Citation | Journal: Nat Commun / Year: 2021 Title: Potent SARS-CoV-2 neutralizing antibodies with protective efficacy against newly emerged mutational variants. Authors: Tingting Li / Xiaojian Han / Chenjian Gu / Hangtian Guo / Huajun Zhang / Yingming Wang / Chao Hu / Kai Wang / Fengjiang Liu / Feiyang Luo / Yanan Zhang / Jie Hu / Wang Wang / Shenglong Li / ...Authors: Tingting Li / Xiaojian Han / Chenjian Gu / Hangtian Guo / Huajun Zhang / Yingming Wang / Chao Hu / Kai Wang / Fengjiang Liu / Feiyang Luo / Yanan Zhang / Jie Hu / Wang Wang / Shenglong Li / Yanan Hao / Meiying Shen / Jingjing Huang / Yingyi Long / Shuyi Song / Ruixin Wu / Song Mu / Qian Chen / Fengxia Gao / Jianwei Wang / Shunhua Long / Luo Li / Yang Wu / Yan Gao / Wei Xu / Xia Cai / Di Qu / Zherui Zhang / Hongqing Zhang / Na Li / Qingzhu Gao / Guiji Zhang / Changlong He / Wei Wang / Xiaoyun Ji / Ni Tang / Zhenghong Yuan / Youhua Xie / Haitao Yang / Bo Zhang / Ailong Huang / Aishun Jin / Abstract: Accumulating mutations in the SARS-CoV-2 Spike (S) protein can increase the possibility of immune escape, challenging the present COVID-19 prophylaxis and clinical interventions. Here, 3 receptor ...Accumulating mutations in the SARS-CoV-2 Spike (S) protein can increase the possibility of immune escape, challenging the present COVID-19 prophylaxis and clinical interventions. Here, 3 receptor binding domain (RBD) specific monoclonal antibodies (mAbs), 58G6, 510A5 and 13G9, with high neutralizing potency blocking authentic SARS-CoV-2 virus display remarkable efficacy against authentic B.1.351 virus. Surprisingly, structural analysis has revealed that 58G6 and 13G9 both recognize the steric region S on the RBD, overlapping the E484K mutation presented in B.1.351. Also, 58G6 directly binds to another region S in the RBD. Significantly, 58G6 and 510A5 both demonstrate prophylactic efficacy against authentic SARS-CoV-2 and B.1.351 viruses in the transgenic mice expressing human ACE2 (hACE2), protecting weight loss and reducing virus loads. Together, we have evidenced 2 potent neutralizing Abs with unique mechanism targeting authentic SARS-CoV-2 mutants, which can be promising candidates to fulfill the urgent needs for the prolonged COVID-19 pandemic. | ||||||
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 | 7e3k.cif.gz | 732.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7e3k.ent.gz | 607.4 KB | Display | PDB format |
PDBx/mmJSON format | 7e3k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7e3k_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7e3k_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7e3k_validation.xml.gz | 112.1 KB | Display | |
Data in CIF | 7e3k_validation.cif.gz | 174.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e3/7e3k ftp://data.pdbj.org/pub/pdb/validation_reports/e3/7e3k | HTTPS FTP |
-Related structure data
Related structure data | 30982MC 7e3lC 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: 142319.219 Da / Num. of mol.: 3 / Mutation: R682G, R683S, R685S, K986P, V987P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2 #2: Antibody | Mass: 23563.473 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) #3: Antibody | Mass: 23587.186 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) #4: 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 (recombinant) |
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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 |
-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: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 52880 / Num. of class averages: 1 / Symmetry type: POINT |