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Yorodumi- PDB-8dxs: Cryo-EM structure of RBD-directed neutralizing antibody P2B4 in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dxs | ||||||
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Title | Cryo-EM structure of RBD-directed neutralizing antibody P2B4 in complex with prefusion SARS-CoV-2 spike glycoprotein | ||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / Neutralizing antibody / Fusion protein / Spike glycoprotein / COVID-19 / RBD / RBD-directed antibody / P2B4 / Viral protein / IMMUNE SYSTEM / Viral Protein-IMMUNE SYSTEM 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 / 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: 3.76 Å | ||||||
Authors | Reddem, E.R. / Shapiro, L. | ||||||
Funding support | China, 1items
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Citation | Journal: Emerg Microbes Infect / Year: 2023 Title: Structural insights into broadly neutralizing antibodies elicited by hybrid immunity against SARS-CoV-2. Authors: Mengxiao Luo / Biao Zhou / Eswar R Reddem / Bingjie Tang / Bohao Chen / Runhong Zhou / Hang Liu / Lihong Liu / Phinikoula S Katsamba / Ka-Kit Au / Hiu-On Man / Kelvin Kai-Wang To / Kwok-Yung ...Authors: Mengxiao Luo / Biao Zhou / Eswar R Reddem / Bingjie Tang / Bohao Chen / Runhong Zhou / Hang Liu / Lihong Liu / Phinikoula S Katsamba / Ka-Kit Au / Hiu-On Man / Kelvin Kai-Wang To / Kwok-Yung Yuen / Lawrence Shapiro / Shangyu Dang / David D Ho / Zhiwei Chen / Abstract: Increasing spread by SARS-CoV-2 Omicron variants challenges existing vaccines and broadly reactive neutralizing antibodies (bNAbs) against COVID-19. Here we determine the diversity, potency, breadth ...Increasing spread by SARS-CoV-2 Omicron variants challenges existing vaccines and broadly reactive neutralizing antibodies (bNAbs) against COVID-19. Here we determine the diversity, potency, breadth and structural insights of bNAbs derived from memory B cells of BNT162b2-vaccinee after homogeneous Omicron BA.1 breakthrough infection. The infection activates diverse memory B cell clonotypes for generating potent class I/II and III bNAbs with new epitopes mapped to the receptor-binding domain (RBD). The top eight bNAbs neutralize wildtype and BA.1 potently but display divergent IgH/IgL sequences and neuralization profiles against other variants of concern (VOCs). Two of them (P2D9 and P3E6) belonging to class III NAbs display comparable potency against BA.4/BA.5, although structural analysis reveals distinct modes of action. P3E6 neutralizes all variants tested through a unique bivalent interaction with two RBDs. Our findings provide new insights into hybrid immunity on BNT162b2-induced diverse memory B cells in response to Omicron breakthrough infection for generating diverse bNAbs with distinct structural basis. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dxs.cif.gz | 679.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dxs.ent.gz | 555.4 KB | Display | PDB format |
PDBx/mmJSON format | 8dxs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dxs_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 8dxs_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 8dxs_validation.xml.gz | 109 KB | Display | |
Data in CIF | 8dxs_validation.cif.gz | 166.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dx/8dxs ftp://data.pdbj.org/pub/pdb/validation_reports/dx/8dxs | HTTPS FTP |
-Related structure data
Related structure data | 27775MC 7ykjC 8dw9C 8dwaC 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: 142399.375 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2 #2: Antibody | Mass: 24474.297 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: 22836.404 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 | 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 | Name: Prefusion SARS-CoV-2 spike glycoprotein in complex with P2B4 Fab Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 4.5 |
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: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 42 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||
3D reconstruction | Resolution: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 93569 / Symmetry type: POINT | ||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT |