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Open data
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Basic information
Entry | Database: PDB / ID: 7m8j | ||||||
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Title | SARS-CoV-2 S-NTD + Fab CM25 | ||||||
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![]() | VIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / CM25 / NTD / Fab / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
Function / homology | ![]() 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 | ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.48 Å | ||||||
![]() | Johnson, N.V. / Mclellan, J.S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Prevalent, protective, and convergent IgG recognition of SARS-CoV-2 non-RBD spike epitopes. Authors: William N Voss / Yixuan J Hou / Nicole V Johnson / George Delidakis / Jin Eyun Kim / Kamyab Javanmardi / Andrew P Horton / Foteini Bartzoka / Chelsea J Paresi / Yuri Tanno / Chia-Wei Chou / ...Authors: William N Voss / Yixuan J Hou / Nicole V Johnson / George Delidakis / Jin Eyun Kim / Kamyab Javanmardi / Andrew P Horton / Foteini Bartzoka / Chelsea J Paresi / Yuri Tanno / Chia-Wei Chou / Shawn A Abbasi / Whitney Pickens / Katia George / Daniel R Boutz / Dalton M Towers / Jonathan R McDaniel / Daniel Billick / Jule Goike / Lori Rowe / Dhwani Batra / Jan Pohl / Justin Lee / Shivaprakash Gangappa / Suryaprakash Sambhara / Michelle Gadush / Nianshuang Wang / Maria D Person / Brent L Iverson / Jimmy D Gollihar / John M Dye / Andrew S Herbert / Ilya J Finkelstein / Ralph S Baric / Jason S McLellan / George Georgiou / Jason J Lavinder / Gregory C Ippolito / ![]() Abstract: The molecular composition and binding epitopes of the immunoglobulin G (IgG) antibodies that circulate in blood plasma after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are ...The molecular composition and binding epitopes of the immunoglobulin G (IgG) antibodies that circulate in blood plasma after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are unknown. Proteomic deconvolution of the IgG repertoire to the spike glycoprotein in convalescent subjects revealed that the response is directed predominantly (>80%) against epitopes residing outside the receptor binding domain (RBD). In one subject, just four IgG lineages accounted for 93.5% of the response, including an amino (N)-terminal domain (NTD)-directed antibody that was protective against lethal viral challenge. Genetic, structural, and functional characterization of a multidonor class of "public" antibodies revealed an NTD epitope that is recurrently mutated among emerging SARS-CoV-2 variants of concern. These data show that "public" NTD-directed and other non-RBD plasma antibodies are prevalent and have implications for SARS-CoV-2 protection and antibody escape. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 152 KB | Display | ![]() |
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PDB format | ![]() | 125.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 976 KB | Display | ![]() |
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Full document | ![]() | 980.7 KB | Display | |
Data in XML | ![]() | 36.3 KB | Display | |
Data in CIF | ![]() | 50.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 23717MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 29297.074 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: S, 2 / Production host: ![]() |
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#2: Antibody | Mass: 13091.598 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Antibody | Mass: 11381.535 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-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: Complex of SARS-CoV-2 S-ECD with CM25 Fab / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | |||||||||||||||
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Source (natural) |
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Source (recombinant) | Organism: ![]() | |||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Sample was monodisperse. All S proteins had 3 Fabs bound. | |||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3 | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: -4 force, 3 s blot |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 80 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Particle selection | Num. of particles selected: 330310 |
3D reconstruction | Resolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 215510 / Symmetry type: POINT |