7S0B | pdb_00007s0b

Structure of the SARS-CoV-2 RBD in complex with neutralizing antibody N-612-056

• PDB DOI: https://doi.org/10.2210/pdb7S0B/pdb

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


• Deposited: 2021-08-30 Released: 2021-10-06 
• Deposition Author(s): Tanaka, S., Barnes, C.O., Bjorkman, P.J.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.260 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display.

Tanaka, S., Olson, C.A., Barnes, C.O., Higashide, W., Gonzalez, M., Taft, J., Richardson, A., Martin-Fernandez, M., Bogunovic, D., Gnanapragasam, P.N.P., Bjorkman, P.J., Spilman, P., Niazi, K., Rabizadeh, S., Soon-Shiong, P.

(2022) Cell Rep 38: 110348-110348

• PubMed: 35114110 
• DOI: https://doi.org/10.1016/j.celrep.2022.110348
• Primary Citation Related Structures: 
  7S0B, 7S0C, 7S0D, 7S0E


• PubMed Abstract: 
  

  The increasing prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with the ability to escape existing humoral protection conferred by previous infection and/or immunization necessitates the discovery of broadly reactive neutralizing antibodies (nAbs). Utilizing mRNA display, we identify a set of antibodies against SARS-CoV-2 spike (S) proteins and characterize the structures of nAbs that recognize epitopes in the S1 subunit of the S glycoprotein. These structural studies reveal distinct binding modes for several antibodies, including the targeting of rare cryptic epitopes in the receptor-binding domain (RBD) of S that interact with angiotensin-converting enzyme 2 (ACE2) to initiate infection, as well as the S1 subdomain 1. Further, we engineer a potent ACE2-blocking nAb to sustain binding to S RBD with the E484K and L452R substitutions found in multiple SARS-CoV-2 variants. We demonstrate that mRNA display is an approach for the rapid identification of nAbs that can be used in combination to combat emerging SARS-CoV-2 variants.

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Organizational Affiliation: 
• ImmunityBio, Inc., 9920 Jefferson Boulevard, Culver City, CA 90232, USA.
ImmunityBio, Inc., 9920 Jefferson Boulevard, Culver City, CA 90232, USA. Electronic address: [e-mail].
Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA.
Center for Inborn Errors of Immunity, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Plaza, New York, NY 10029-5674, USA; Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Plaza, New York, NY 10029-5674, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Plaza, New York, NY 10029-5674, USA.
Center for Inborn Errors of Immunity, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Plaza, New York, NY 10029-5674, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Plaza, New York, NY 10029-5674, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Plaza, New York, NY 10029-5674, USA; Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Plaza, New York, NY 10029-5674, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1 Gustave Lane, Levy Plaza, New York, NY 10029-5674, USA.
ImmunityBio, Inc., 9920 Jefferson Boulevard, Culver City, CA 90232, USA. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 145.18 kDa 
• Atom Count: 9,828 
• Modeled Residue Count: 1,260 
• Deposited Residue Count: 1,326 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-612-056 Fab Heavy Chain	A, C	228	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
N-612-056 Light Chain	B, D	214	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	E, F	221	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

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.260 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.297	α = 90
b = 153.656	β = 90
c = 96.59	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-10-06 
Deposition Author(s): Tanaka, S., Barnes, C.O., Bjorkman, P.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	P01-AI138938-S1

Revision History  

• Version 1.0: 2021-10-06
  Type: Initial release
  
• Version 1.1: 2022-03-16
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary