8D48

sd1.040 Fab in complex with SARS-CoV-2 Spike 2P glycoprotein


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Human neutralizing antibodies to cold linear epitopes and to subdomain 1 of SARS-CoV-2.

Bianchini, F.Crivelli, V.Abernathy, M.E.Guerra, C.Palus, M.Muri, J.Marcotte, H.Piralla, A.Pedotti, M.Gasparo, R.Simonelli, L.Matkovic, M.Toscano, C.Biggiogero, M.Calvaruso, V.Svoboda, P.Rincon, T.C.Fava, T.Podesvova, L.Shanbhag, A.A.Celoria, A.Sgrignani, J.Stefanik, M.Honig, V.Pranclova, V.Michalcikova, T.Prochazka, J.Guerrini, G.Mehn, D.Ciabattini, A.Abolhassani, H.Jarrossay, D.Uguccioni, M.Medaglini, D.Pan-Hammarstrom, Q.Calzolai, L.Fernandez, D.Baldanti, F.Franzetti-Pellanda, A.Garzoni, C.Sedlacek, R.Ruzek, D.Varani, L.Cavalli, A.Barnes, C.O.Robbiani, D.F.

(2022) Biorxiv 

  • DOI: 10.1101/2022.11.24.515932
  • Primary Citation of Related Structures:  
    8D47, 8D48

  • PubMed Abstract: 
  • Emergence of SARS-CoV-2 variants diminishes the efficacy of vaccines and antiviral monoclonal antibodies. Continued development of immunotherapies and vaccine immunogens resilient to viral evolution is therefore necessary. Using coldspot-guided antibody discovery, a screening approach that focuses on portions of the virus spike that are both functionally relevant and averse to change, we identified human neutralizing antibodies to highly conserved viral epitopes ...

    Emergence of SARS-CoV-2 variants diminishes the efficacy of vaccines and antiviral monoclonal antibodies. Continued development of immunotherapies and vaccine immunogens resilient to viral evolution is therefore necessary. Using coldspot-guided antibody discovery, a screening approach that focuses on portions of the virus spike that are both functionally relevant and averse to change, we identified human neutralizing antibodies to highly conserved viral epitopes. Antibody fp.006 binds the fusion peptide and cross-reacts against coronaviruses of the four genera , including the nine human coronaviruses, through recognition of a conserved motif that includes the S2' site of proteolytic cleavage. Antibody hr2.016 targets the stem helix and neutralizes SARS-CoV-2 variants. Antibody sd1.040 binds to subdomain 1, synergizes with antibody rbd.042 for neutralization and, like fp.006 and hr2.016, protects mice when present as bispecific antibody. Thus, coldspot-guided antibody discovery reveals donor-derived neutralizing antibodies that are cross-reactive with Orthocoronavirinae , including SARS-CoV-2 variants.


    Organizational Affiliation

    National Biomedical Imaging Center, Peking University, 100871, Beijing, China. gaon@pku.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Spike glycoproteinA1,259Severe acute respiratory syndrome coronavirus 2Mutation(s): 2 
Gene Names: S2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC2
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
sd1.040 Fab heavy chainB [auth H]233Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
sd1.040 Fab light chainC [auth L]220Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth B]2N/AN-Glycosylation Oligosaccharides Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United StatesGT15335

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-25
    Type: Initial release