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Yorodumi- PDB-7whk: The state 3 complex structure of Omicron spike with Bn03 (2-up RB... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7whk | ||||||
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Title | The state 3 complex structure of Omicron spike with Bn03 (2-up RBD, 5 nanobodies) | ||||||
Components |
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Keywords | VIRAL PROTEIN / Omicron / Spike / Nanobody | ||||||
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: 3.01 Å | ||||||
Authors | Zhan, W.Q. / Zhang, X. / Chen, Z.G. / Sun, L. | ||||||
Funding support | China, 1items
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Citation | Journal: Cell / Year: 2022 Title: Broad neutralization of SARS-CoV-2 variants by an inhalable bispecific single-domain antibody. Authors: Cheng Li / Wuqiang Zhan / Zhenlin Yang / Chao Tu / Gaowei Hu / Xiang Zhang / Wenping Song / Shujuan Du / Yuanfei Zhu / Keke Huang / Yu Kong / Meng Zhang / Qiyu Mao / Xiaodan Gu / Yi Zhang / ...Authors: Cheng Li / Wuqiang Zhan / Zhenlin Yang / Chao Tu / Gaowei Hu / Xiang Zhang / Wenping Song / Shujuan Du / Yuanfei Zhu / Keke Huang / Yu Kong / Meng Zhang / Qiyu Mao / Xiaodan Gu / Yi Zhang / Youhua Xie / Qiang Deng / Yuanlin Song / Zhenguo Chen / Lu Lu / Shibo Jiang / Yanling Wu / Lei Sun / Tianlei Ying / Abstract: The effectiveness of SARS-CoV-2 vaccines and therapeutic antibodies have been limited by the continuous emergence of viral variants and by the restricted diffusion of antibodies from circulation into ...The effectiveness of SARS-CoV-2 vaccines and therapeutic antibodies have been limited by the continuous emergence of viral variants and by the restricted diffusion of antibodies from circulation into the sites of respiratory virus infection. Here, we report the identification of two highly conserved regions on the Omicron variant receptor-binding domain recognized by broadly neutralizing antibodies. Furthermore, we generated a bispecific single-domain antibody that was able to simultaneously and synergistically bind these two regions on a single Omicron variant receptor-binding domain as revealed by cryo-EM structures. We demonstrated that this bispecific antibody can be effectively delivered to lung via inhalation administration and exhibits exquisite neutralization breadth and therapeutic efficacy in mouse models of SARS-CoV-2 infections. Importantly, this study also deciphered an uncommon and highly conserved cryptic epitope within the spike trimeric interface that may have implications for the design of broadly protective SARS-CoV-2 vaccines and therapeutics. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7whk.cif.gz | 655.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7whk.ent.gz | 541.9 KB | Display | PDB format |
PDBx/mmJSON format | 7whk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7whk_validation.pdf.gz | 825 KB | Display | wwPDB validaton report |
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Full document | 7whk_full_validation.pdf.gz | 876.4 KB | Display | |
Data in XML | 7whk_validation.xml.gz | 100.3 KB | Display | |
Data in CIF | 7whk_validation.cif.gz | 153 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wh/7whk ftp://data.pdbj.org/pub/pdb/validation_reports/wh/7whk | HTTPS FTP |
-Related structure data
Related structure data | 32503MC 7whiC 7whjC 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: 142506.000 Da / Num. of mol.: 3 / Mutation: hexaPro mutations Source method: isolated from a genetically manipulated source Details: residues 682-685 are substitution at furin cleavage site. T4 fibritin trimerization motif and twin strep II tag and 8 His were introduced at C terminal. Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Variant: omicron / Production host: Homo sapiens (human) / References: UniProt: P0DTC2 #2: Antibody | Mass: 13170.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #3: Protein | Mass: 14195.451 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: Sugar | ChemComp-NAG / Has ligand of interest | N | |
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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: 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: 2500 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 58 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 170469 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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