7N5H | pdb_00007n5h

Cryo-EM structure of broadly neutralizing antibody 2-36 in complex with prefusion SARS-CoV-2 spike glycoprotein

• PDB DOI: https://doi.org/10.2210/pdb7N5H/pdb
• EM Map EMD-24190: 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: 2021-06-05 Released: 2021-11-03 
• Deposition Author(s): Casner, R.G., Cerutti, G., Shapiro, L.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.24 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental

Literature

A monoclonal antibody that neutralizes SARS-CoV-2 variants, SARS-CoV, and other sarbecoviruses.

Wang, P., Casner, R.G., Nair, M.S., Yu, J., Guo, Y., Wang, M., Chan, J.F., Cerutti, G., Iketani, S., Liu, L., Sheng, Z., Chen, Z., Yuen, K.Y., Kwong, P.D., Huang, Y., Shapiro, L., Ho, D.D.

(2022) Emerg Microbes Infect 11: 147-157

• PubMed: 34836485 
• DOI: https://doi.org/10.1080/22221751.2021.2011623
• Primary Citation Related Structures: 
  7N5H


• PubMed Abstract: 
  

  The repeated emergence of highly pathogenic human coronaviruses as well as their evolving variants highlight the need to develop potent and broad-spectrum antiviral therapeutics and vaccines. By screening monoclonal antibodies (mAbs) isolated from COVID-19-convalescent patients, we found one mAb, 2-36, with cross-neutralizing activity against SARS-CoV. We solved the cryo-EM structure of 2-36 in complex with SARS-CoV-2 or SARS-CoV spike, revealing a highly conserved epitope in the receptor-binding domain (RBD). Antibody 2-36 neutralized not only all current circulating SARS-CoV-2 variants and SARS-COV, but also a panel of bat and pangolin sarbecoviruses that can use human angiotensin-converting enzyme 2 (ACE2) as a receptor. We selected 2-36-escape viruses in vitro and confirmed that K378 T in SARS-CoV-2 RBD led to viral resistance. Taken together, 2-36 represents a strategic reserve drug candidate for the prevention and treatment of possible diseases caused by pre-emergent SARS-related coronaviruses. Its epitope defines a promising target for the development of a pan-sarbecovirus vaccine.

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Organizational Affiliation: 
• Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China.
Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, People's Republic of China.
Vaccine Research Center, National Institutes of Health, Bethesda, USA.
Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA.
Division of Infectious Diseases, Department of Internal Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 9-mer - A3B3C3 Pseudo Symmetry: Cyclic - C3  (Explore in 3D)
Pseudo Stoichiometry: Hetero 9-mer - A6B3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: surface plasmon resonance

Macromolecule Content 

• Total Structure Weight: 513.33 kDa 
• Atom Count: 29,691 
• Modeled Residue Count: 3,739 
• Deposited Residue Count: 4,572 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,288	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: 8		Go to GlyGen: P0DTC2-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
2-36 Fab heavy chain	D [auth H], F [auth E], H [auth J]	128	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
2-36 Fab light chain	E [auth L], G [auth F], I [auth K]	108	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J [auth D], K [auth G], L [auth I], M, N, O, P, Q, R, S, T, U, V, W, X, Y	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	AA [auth A], BA [auth A], CA [auth A], DA [auth B], EA [auth B], FA [auth C], GA [auth C], HA [auth C], Z [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: 3.24 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	v2.15
MODEL REFINEMENT	PHENIX	1.18

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-11-03 
Deposition Author(s): Casner, R.G., Cerutti, G., Shapiro, L.

Revision History  

• Version 1.0: 2021-11-03
  Type: Initial release
  
• Version 1.1: 2022-11-16
  Changes: Database references
• Version 1.2: 2024-10-16
  Changes: Data collection, Refinement description, Structure summary