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Yorodumi- PDB-7x29: MERS-CoV spike complex with S41 neutralizing antibody Fab Class2 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7x29 | ||||||
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Title | MERS-CoV spike complex with S41 neutralizing antibody Fab Class2 (1u2d RBD with 2Fab) | ||||||
Components |
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Keywords | VIRAL PROTEIN / receptor binding domain | ||||||
Function / homology | Function and homology information host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / receptor-mediated endocytosis of virus by host cell / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane ...host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / receptor-mediated endocytosis of virus by host cell / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / membrane Similarity search - Function | ||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.49 Å | ||||||
Authors | Zeng, J.W. / Zhang, S.Y. / Zhou, H.X. / Wang, X.W. | ||||||
Funding support | China, 1items
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Citation | Journal: Front Microbiol / Year: 2022 Title: Cryoelectron microscopy structures of a human neutralizing antibody bound to MERS-CoV spike glycoprotein. Authors: Shuyuan Zhang / Wenxv Jia / Jianwei Zeng / Mingxi Li / Ziyi Wang / Haixia Zhou / Linqi Zhang / Xinquan Wang / Abstract: Neutralizing monoclonal antibodies (mAbs) against highly pathogenic coronaviruses represent promising candidates for clinical intervention. Here, we isolated a potent neutralizing monoclonal ...Neutralizing monoclonal antibodies (mAbs) against highly pathogenic coronaviruses represent promising candidates for clinical intervention. Here, we isolated a potent neutralizing monoclonal antibody, MERS-S41, from a yeast displayed scFv library using the S protein as a bait. To uncover the neutralization mechanism, we determined structures of MERS-S41 Fab in complex with the trimeric spike glycoprotein by cryoelectron microscopy (cryo-EM). We observed four distinct classes of the complex structure, which showed that the MERS-S41 Fab bound to the "up" receptor binding domain (RBD) with full saturation and also bound to an accessible partially lifted "down" RBD, providing a structural basis for understanding how mAbs bind to trimeric spike glycoproteins. Structure analysis of the epitope and cell surface staining assays demonstrated that virus entry is blocked predominantly by direct competition with the host receptor, dipeptidyl peptidase-4 (DPP4). | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7x29.cif.gz | 773.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7x29.ent.gz | 623.8 KB | Display | PDB format |
PDBx/mmJSON format | 7x29.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7x29_validation.pdf.gz | 787.2 KB | Display | wwPDB validaton report |
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Full document | 7x29_full_validation.pdf.gz | 847.4 KB | Display | |
Data in XML | 7x29_validation.xml.gz | 100.9 KB | Display | |
Data in CIF | 7x29_validation.cif.gz | 159.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x2/7x29 ftp://data.pdbj.org/pub/pdb/validation_reports/x2/7x29 | HTTPS FTP |
-Related structure data
Related structure data | 32962MC 7x25C 7x26C 7x28C 7x2aC 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: 148570.266 Da / Num. of mol.: 3 / Mutation: V1060P, l1061P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Production host: Trichoplusia ni (cabbage looper) / References: UniProt: K0BRG7 #2: Antibody | Mass: 23251.098 Da / Num. of mol.: 2 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: 23095.535 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) Has protein modification | 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 |
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.2 | ||||||||||||||||||||||||
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: OTHER / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.49 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 424969 / Symmetry type: POINT |