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- PDB-7sb4: Structure of OC43 spike in complex with polyclonal Fab2 (Donor 1412) -
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Open data
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Basic information
Entry | Database: PDB / ID: 7sb4 | |||||||||
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Title | Structure of OC43 spike in complex with polyclonal Fab2 (Donor 1412) | |||||||||
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![]() | VIRAL PROTEIN/Immune System / HCoV / spike / OC43 / polyclonal antibody / EMPEM / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex | |||||||||
Function / homology | ![]() endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to 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 | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.7 Å | |||||||||
![]() | Bangaru, S. / Antanasijevic, A. / Ward, A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural mapping of antibody landscapes to human betacoronavirus spike proteins. Authors: Sandhya Bangaru / Aleksandar Antanasijevic / Nurgun Kose / Leigh M Sewall / Abigail M Jackson / Naveenchandra Suryadevara / Xiaoyan Zhan / Jonathan L Torres / Jeffrey Copps / Alba Torrents ...Authors: Sandhya Bangaru / Aleksandar Antanasijevic / Nurgun Kose / Leigh M Sewall / Abigail M Jackson / Naveenchandra Suryadevara / Xiaoyan Zhan / Jonathan L Torres / Jeffrey Copps / Alba Torrents de la Peña / James E Crowe / Andrew B Ward / ![]() Abstract: Preexisting immunity against seasonal coronaviruses (CoVs) represents an important variable in predicting antibody responses and disease severity to severe acute respiratory syndrome CoV-2 (SARS-CoV- ...Preexisting immunity against seasonal coronaviruses (CoVs) represents an important variable in predicting antibody responses and disease severity to severe acute respiratory syndrome CoV-2 (SARS-CoV-2) infections. We used electron microscopy-based polyclonal epitope mapping (EMPEM) to characterize the antibody specificities against β-CoV spike proteins in prepandemic (PP) sera or SARS-CoV-2 convalescent (SC) sera. We observed that most PP sera had antibodies specific to seasonal human CoVs (HCoVs) OC43 and HKU1 spike proteins while the SC sera showed reactivity across all human β-CoVs. Detailed molecular mapping of spike-antibody complexes revealed epitopes that were differentially targeted by preexisting antibodies and SC serum antibodies. Our studies provide an antigenic landscape to β-HCoV spikes in the general population serving as a basis for cross-reactive epitope analyses in SARS-CoV-2-infected individuals. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 721.5 KB | Display | ![]() |
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PDB format | ![]() | 605.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 109 KB | Display | |
Data in CIF | ![]() | 167 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 24969MC ![]() 7sb3C ![]() 7sb5C ![]() 7sbvC ![]() 7sbwC ![]() 7sbxC ![]() 7sbyC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-Protein / Antibody / Non-polymers , 3 types, 8 molecules ACBHL![](data/chem/img/8Z9.gif)
![](data/chem/img/8Z9.gif)
#1: Protein | Mass: 151119.891 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Antibody | Mass: 9634.868 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #6: Chemical | |
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-Sugars , 3 types, 42 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / |
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-Details
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 |
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Sample preparation
Component | Name: Structure of OC43 spike in complex with polyclonal Fab2 (Donor 1412) Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT | ||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||
Source (natural) | Organism: ![]() | ||||||||||||
Source (recombinant) | Organism: ![]() | ||||||||||||
Buffer solution | pH: 7.4 / Details: TBS 1X | ||||||||||||
Buffer component |
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Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
Specimen support | Grid material: GOLD / Grid type: UltrAuFoil R1.2/1.3 | ||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 29000 X / Nominal defocus max: 1300 nm / Nominal defocus min: 300 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 10 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 2321 |
Image scans | Movie frames/image: 40 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7005 / Algorithm: BACK PROJECTION / Symmetry type: POINT |