|Entry||Database: EMDB / ID: EMD-22507|
|Title||SARS-CoV-2 spike in complex with the S2H14 neutralizing antibody Fab fragment (two receptor-binding domains open)|
|Sample||SARS-CoV-2 spike in complex with the S2H14 neutralizing antibody Fab fragment (two receptor-binding domains open)|
|Biological species||Severe acute respiratory syndrome coronavirus 2 / Homo sapiens (human)|
|Method||single particle reconstruction / cryo EM / Resolution: 7.8 Å|
|Authors||Park YJ / Tortorici MA / Walls AC / Czudnochowski N / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Snell G / Veesler D|
|Funding support|| United States, 1 items |
|Citation||Journal: Cell / Year: 2020|
Title: Mapping Neutralizing and Immunodominant Sites on the SARS-CoV-2 Spike Receptor-Binding Domain by Structure-Guided High-Resolution Serology.
Authors: Luca Piccoli / Young-Jun Park / M Alejandra Tortorici / Nadine Czudnochowski / Alexandra C Walls / Martina Beltramello / Chiara Silacci-Fregni / Dora Pinto / Laura E Rosen / John E Bowen / ...Authors: Luca Piccoli / Young-Jun Park / M Alejandra Tortorici / Nadine Czudnochowski / Alexandra C Walls / Martina Beltramello / Chiara Silacci-Fregni / Dora Pinto / Laura E Rosen / John E Bowen / Oliver J Acton / Stefano Jaconi / Barbara Guarino / Andrea Minola / Fabrizia Zatta / Nicole Sprugasci / Jessica Bassi / Alessia Peter / Anna De Marco / Jay C Nix / Federico Mele / Sandra Jovic / Blanca Fernandez Rodriguez / Sneha V Gupta / Feng Jin / Giovanni Piumatti / Giorgia Lo Presti / Alessandra Franzetti Pellanda / Maira Biggiogero / Maciej Tarkowski / Matteo S Pizzuto / Elisabetta Cameroni / Colin Havenar-Daughton / Megan Smithey / David Hong / Valentino Lepori / Emiliano Albanese / Alessandro Ceschi / Enos Bernasconi / Luigia Elzi / Paolo Ferrari / Christian Garzoni / Agostino Riva / Gyorgy Snell / Federica Sallusto / Katja Fink / Herbert W Virgin / Antonio Lanzavecchia / Davide Corti / David Veesler /
Abstract: Analysis of the specificity and kinetics of neutralizing antibodies (nAbs) elicited by SARS-CoV-2 infection is crucial for understanding immune protection and identifying targets for vaccine design. ...Analysis of the specificity and kinetics of neutralizing antibodies (nAbs) elicited by SARS-CoV-2 infection is crucial for understanding immune protection and identifying targets for vaccine design. In a cohort of 647 SARS-CoV-2-infected subjects, we found that both the magnitude of Ab responses to SARS-CoV-2 spike (S) and nucleoprotein and nAb titers correlate with clinical scores. The receptor-binding domain (RBD) is immunodominant and the target of 90% of the neutralizing activity present in SARS-CoV-2 immune sera. Whereas overall RBD-specific serum IgG titers waned with a half-life of 49 days, nAb titers and avidity increased over time for some individuals, consistent with affinity maturation. We structurally defined an RBD antigenic map and serologically quantified serum Abs specific for distinct RBD epitopes leading to the identification of two major receptor-binding motif antigenic sites. Our results explain the immunodominance of the receptor-binding motif and will guide the design of COVID-19 vaccines and therapeutics.
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_22507.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.16 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Additional map: Unsharpened map
-Entire SARS-CoV-2 spike in complex with the S2H14 neutralizing antibody ...
|Entire||Name: SARS-CoV-2 spike in complex with the S2H14 neutralizing antibody Fab fragment (two receptor-binding domains open)|
Number of Components: 3
-Component #1: protein, SARS-CoV-2 spike in complex with the S2H14 neutralizing ...
|Protein||Name: SARS-CoV-2 spike in complex with the S2H14 neutralizing antibody Fab fragment (two receptor-binding domains open)|
Recombinant expression: No
-Component #2: protein, spike glycoprotein
|Protein||Name: spike glycoproteinSpike protein / Recombinant expression: No|
|Source||Species: Severe acute respiratory syndrome coronavirus 2|
|Source (engineered)||Expression System: Homo sapiens (human)|
-Component #3: protein, S2H14 neutralizing antibody Fab fragment
|Protein||Name: S2H14 neutralizing antibody Fab fragment / Recombinant expression: No|
|Source||Species: Homo sapiens (human)|
|Source (engineered)||Expression System: Cricetulus griseus (Chinese hamster)|
|Specimen||Specimen State: Particle / Method: cryo EM|
|Sample solution||pH: 8|
|Vitrification||Cryogen Name: ETHANE|
-Electron microscopy imaging
|Imaging||Microscope: TFS GLACIOS|
|Electron gun||Electron Source: FIELD EMISSION GUN / Accelerating Voltage: 200 kV / Electron Dose: 60 e/Å2 / Illumination Mode: FLOOD BEAM|
|Lens||Imaging Mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Processing||Method: single particle reconstruction / Applied Symmetry: C1 (asymmetric) / Number of Projections: 9957|
|3D reconstruction||Software: cryoSPARC / Resolution: 7.8 Å / Resolution Method: FSC 0.143 CUT-OFF|
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