7N62 | pdb_00007n62

SARS-CoV-2 Spike (2P) in complex with C12C9 Fab (NTD local reconstruction)

• PDB DOI: https://doi.org/10.2210/pdb7N62/pdb
• EM Map EMD-24192: EMDB EMDataResource

• Classification: VIRAL PROTEIN/Immune System
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2021-06-07 Released: 2021-08-04 
• Deposition Author(s): Windsor, I.W., Jenni, S., Bajic, G., Tong, P., Gautam, A.K., Wesemann, D.R., Harrison, S.C.

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental

Literature

Memory B cell repertoire for recognition of evolving SARS-CoV-2 spike.

Tong, P., Gautam, A., Windsor, I., Travers, M., Chen, Y., Garcia, N., Whiteman, N.B., McKay, L.G.A., Lelis, F.J.N., Habibi, S., Cai, Y., Rennick, L.J., Duprex, W.P., McCarthy, K.R., Lavine, C.L., Zuo, T., Lin, J., Zuiani, A., Feldman, J., MacDonald, E.A., Hauser, B.M., Griffths, A., Seaman, M.S., Schmidt, A.G., Chen, B., Neuberg, D., Bajic, G., Harrison, S.C., Wesemann, D.R.

(2021) bioRxiv 

• PubMed: 33758863 
• DOI: https://doi.org/10.1101/2021.03.10.434840
• Primary Citation Related Structures: 
  7N62, 7N64


• PubMed Abstract: 
  

  Memory B cell reserves can generate protective antibodies against repeated SARS-CoV-2 infections, but with an unknown reach from original infection to antigenically drifted variants. We charted memory B cell receptor-encoded monoclonal antibodies (mAbs) from 19 COVID-19 convalescent subjects against SARS-CoV-2 spike (S) and found 7 major mAb competition groups against epitopes recurrently targeted across individuals. Inclusion of published and newly determined structures of mAb-S complexes identified corresponding epitopic regions. Group assignment correlated with cross-CoV-reactivity breadth, neutralization potency, and convergent antibody signatures. mAbs that competed for binding the original S isolate bound differentially to S variants, suggesting the protective importance of otherwise-redundant recognition. The results furnish a global atlas of the S-specific memory B cell repertoire and illustrate properties conferring robustness against emerging SARS-CoV-2 variants.

---

Organizational Affiliation: 
• Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
Department of Microbiology, Boston University School of Medicine, Boston, MA 02115, USA.
National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02115, USA.
Laboratory of Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA.
The Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261.
The Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh PA.
Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA.
Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA.
Department of Microbiology, Harvard Medical School, Boston MA 02115.
Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA.
Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
Howard Hughes Medical Institute, Boston, MA 02115, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 190.2 kDa 
• Atom Count: 5,613 
• Modeled Residue Count: 712 
• Deposited Residue Count: 1,715 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A	1,273	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2
Glycosylation
Glycosylation Sites: 5		Go to GlyGen: P0DTC2-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
C12C9 Fab heavy chain	B [auth H]	228	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
C12C9 Fab light chain	C [auth L]	214	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.1
MODEL REFINEMENT	PHENIX	1.18.2-3874

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-08-04 
Deposition Author(s): Windsor, I.W., Jenni, S., Bajic, G., Tong, P., Gautam, A.K., Wesemann, D.R., Harrison, S.C.

Revision History  

• Version 1.0: 2021-08-04
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Data collection, Database references, Refinement description, Structure summary