7SD5 | pdb_00007sd5

Crystallographic structure of neutralizing antibody 10-40 in complex with SARS-CoV-2 spike receptor binding domain

• PDB DOI: https://doi.org/10.2210/pdb7SD5/pdb

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


• Deposited: 2021-09-29 Released: 2022-04-27 
• Deposition Author(s): Reddem, E.R., Casner, R.G., Shapiro, L.
• Funding Organization(s): Jack Ma Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 
  0.206 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

An antibody class with a common CDRH3 motif broadly neutralizes sarbecoviruses.

Liu, L., Iketani, S., Guo, Y., Reddem, E.R., Casner, R.G., Nair, M.S., Yu, J., Chan, J.F., Wang, M., Cerutti, G., Li, Z., Morano, N.C., Castagna, C.D., Corredor, L., Chu, H., Yuan, S., Poon, V.K., Chan, C.C., Chen, Z., Luo, Y., Cunningham, M., Chavez, A., Yin, M.T., Perlin, D.S., Tsuji, M., Yuen, K.Y., Kwong, P.D., Sheng, Z., Huang, Y., Shapiro, L., Ho, D.D.

(2022) Sci Transl Med 14: eabn6859-eabn6859

• PubMed: 35438546 
• DOI: https://doi.org/10.1126/scitranslmed.abn6859
• Primary Citation Related Structures: 
  7SD5, 7SI2, 7TTM, 7TTX, 7TTY


• PubMed Abstract: 
  

  The devastation caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has made clear the importance of pandemic preparedness. To address future zoonotic outbreaks due to related viruses in the sarbecovirus subgenus, we identified a human monoclonal antibody, 10-40, that neutralized or bound all sarbecoviruses tested in vitro and protected against SARS-CoV-2 and SARS-CoV in vivo. Comparative studies with other receptor-binding domain (RBD)-directed antibodies showed 10-40 to have the greatest breadth against sarbecoviruses, suggesting that 10-40 is a promising agent for pandemic preparedness. Moreover, structural analyses on 10-40 and similar antibodies not only defined an epitope cluster in the inner face of the RBD that is well conserved among sarbecoviruses but also uncovered a distinct antibody class with a common CDRH3 motif. Our analyses also suggested that elicitation of this class of antibodies may not be overly difficult, an observation that bodes well 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 10032, USA.
Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA.
Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China.
Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, Hong Kong Special Administrative Region, China.
Institute of Comparative Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA.
AIDS Institute, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China.
Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ 07110, USA.
Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA.
Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 75.78 kDa 
• Atom Count: 5,628 
• Modeled Residue Count: 633 
• Deposited Residue Count: 691 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A	239	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: 1		Go to GlyGen: P0DTC2-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
10-40 Heavy chain	B [auth H]	236	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
10-40 Light chain	C [auth L]	216	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	D [auth B]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free:  0.206 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.756	α = 90
b = 79.845	β = 90
c = 118.864	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-04-27 
Deposition Author(s): Reddem, E.R., Casner, R.G., Shapiro, L.

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Funding Organization	Location	Grant Number
Jack Ma Foundation	China	--

Revision History  

• Version 1.0: 2022-04-27
  Type: Initial release
  
• Version 1.1: 2022-05-04
  Changes: Database references
• Version 1.2: 2022-06-08
  Changes: Database references
• Version 1.3: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary