+Open data
-Basic information
Entry | Database: PDB / ID: 8khd | ||||||
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Title | The interface structure of Omicron RBD binding to 5817 Fab | ||||||
Components |
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Keywords | VIRAL PROTEIN / SARS-CoV-2 / Omicron / RBD / Fab | ||||||
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 / 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 | Homo sapiens (human) Severe acute respiratory syndrome coronavirus 2 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
Authors | Cao, L. / Wang, X. | ||||||
Funding support | 1items
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Citation | Journal: Cell Rep / Year: 2024 Title: Identification of a broad sarbecovirus neutralizing antibody targeting a conserved epitope on the receptor-binding domain. Authors: Yanqun Wang / Zhaoyong Zhang / Minnan Yang / Xinyi Xiong / Qihong Yan / Lei Cao / Peilan Wei / Yuting Zhang / Lu Zhang / Kexin Lv / Jiantao Chen / Xuesong Liu / Xiaochu Zhao / Juxue Xiao / ...Authors: Yanqun Wang / Zhaoyong Zhang / Minnan Yang / Xinyi Xiong / Qihong Yan / Lei Cao / Peilan Wei / Yuting Zhang / Lu Zhang / Kexin Lv / Jiantao Chen / Xuesong Liu / Xiaochu Zhao / Juxue Xiao / Shengnan Zhang / Airu Zhu / Mian Gan / Jingjun Zhang / Ruoxi Cai / Jianfen Zhuo / Yanjun Zhang / Haiyue Rao / Bin Qu / Yuanyuan Zhang / Lei Chen / Jun Dai / Linling Cheng / Qingtao Hu / Yaoqing Chen / Huibin Lv / Ray T Y So / Malik Peiris / Jingxian Zhao / Xiaoqing Liu / Chris Ka Pun Mok / Xiangxi Wang / Jincun Zhao / Abstract: Omicron, as the emerging variant with enhanced vaccine tolerance, has sharply disrupted most therapeutic antibodies. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) belongs to the ...Omicron, as the emerging variant with enhanced vaccine tolerance, has sharply disrupted most therapeutic antibodies. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) belongs to the subgenus Sarbecovirus, members of which share high sequence similarity. Herein, we report one sarbecovirus antibody, 5817, which has broad-spectrum neutralization capacity against SARS-CoV-2 variants of concern (VOCs) and SARS-CoV, as well as related bat and pangolin viruses. 5817 can hardly compete with six classes of receptor-binding-domain-targeted antibodies grouped by structural classifications. No obvious impairment in the potency is detected against SARS-CoV-2 Omicron and subvariants. The cryoelectron microscopy (cryo-EM) structure of neutralizing antibody 5817 in complex with Omicron spike reveals a highly conserved epitope, only existing at the receptor-binding domain (RBD) open state. Prophylactic and therapeutic administration of 5817 potently protects mice from SARS-CoV-2 Beta, Delta, Omicron, and SARS-CoV infection. This study reveals a highly conserved cryptic epitope targeted by a broad sarbecovirus neutralizing antibody, which would be beneficial to meet the potential threat of pre-emergent SARS-CoV-2 VOCs. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8khd.cif.gz | 88.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8khd.ent.gz | 65 KB | Display | PDB format |
PDBx/mmJSON format | 8khd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8khd_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8khd_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8khd_validation.xml.gz | 28.1 KB | Display | |
Data in CIF | 8khd_validation.cif.gz | 37.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kh/8khd ftp://data.pdbj.org/pub/pdb/validation_reports/kh/8khd | HTTPS FTP |
-Related structure data
Related structure data | 37241MC 8khcC 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: Antibody | Mass: 13387.045 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 11470.526 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
#3: Protein | Mass: 22836.854 Da / Num. of mol.: 1 / Fragment: RBD Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 Production host: Severe acute respiratory syndrome coronavirus 2 References: UniProt: P0DTC2 |
#4: Sugar | ChemComp-NAG / |
Has ligand of interest | Y |
-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 | Name: The interface structure of Omicron RBD binding to 5817 Fab Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.5 |
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: 2000 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 45 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: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5129 / Symmetry type: POINT | ||||||||||||||||||||||||
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