7K9Z | pdb_00007k9z

Crystal structure of SARS-CoV-2 receptor binding domain in complex with the Fab fragments of neutralizing antibodies 298 and 52

• PDB DOI: https://doi.org/10.2210/pdb7K9Z/pdb

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


• Deposited: 2020-09-29 Released: 2020-10-28 
• Deposition Author(s): Newton, J.C., Kucharska, I., Rujas, E., Cui, H., Julien, J.P.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada), Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 
  0.287 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.261 (Depositor), 0.263 (DCC) 
• R-Value Observed: 
  0.263 (Depositor) 

Starting Models: experimental

Literature

Multivalency transforms SARS-CoV-2 antibodies into ultrapotent neutralizers.

Rujas, E., Kucharska, I., Tan, Y.Z., Benlekbir, S., Cui, H., Zhao, T., Wasney, G.A., Budylowski, P., Guvenc, F., Newton, J.C., Sicard, T., Semesi, A., Muthuraman, K., Nouanesengsy, A., Aschner, C.B., Prieto, K., Bueler, S.A., Youssef, S., Liao-Chan, S., Glanville, J., Christie-Holmes, N., Mubareka, S., Gray-Owen, S.D., Rubinstein, J.L., Treanor, B., Julien, J.P.

(2021) Nat Commun 12: 3661-3661

• PubMed: 34135340 
• DOI: https://doi.org/10.1038/s41467-021-23825-2
• Primary Citation Related Structures: 
  7K9Z


• PubMed Abstract: 
  

  SARS-CoV-2, the virus responsible for COVID-19, has caused a global pandemic. Antibodies can be powerful biotherapeutics to fight viral infections. Here, we use the human apoferritin protomer as a modular subunit to drive oligomerization of antibody fragments and transform antibodies targeting SARS-CoV-2 into exceptionally potent neutralizers. Using this platform, half-maximal inhibitory concentration (IC ₅₀ ) values as low as 9 × 10 ^{- 14} M are achieved as a result of up to 10,000-fold potency enhancements compared to corresponding IgGs. Combination of three different antibody specificities and the fragment crystallizable (Fc) domain on a single multivalent molecule conferred the ability to overcome viral sequence variability together with outstanding potency and IgG-like bioavailability. The MULTi-specific, multi-Affinity antiBODY (Multabody or MB) platform thus uniquely leverages binding avidity together with multi-specificity to deliver ultrapotent and broad neutralizers against SARS-CoV-2. The modularity of the platform also makes it relevant for rapid evaluation against other infectious diseases of global health importance. Neutralizing antibodies are a promising therapeutic for SARS-CoV-2.

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Organizational Affiliation: 
• Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada.
Department of Biochemistry, University of Toronto, Toronto, ON, Canada.
Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain.
Department of Immunology, University of Toronto, Toronto, ON, Canada.
The Structural & Biophysical Core Facility, The Hospital for Sick Children Research Institute, Toronto, ON, Canada.
Combined Containment Level 3 Unit, University of Toronto, Toronto, ON, Canada.
Institute of Medical Science, University of Toronto, Toronto, ON, Canada.
Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
Distributed Bio, South San Francisco, CA, USA.
Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
Sunnybrook Health Sciences Centre, Toronto, ON, Canada.
Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada.
Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada.
Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada. [e-mail].
Department of Biochemistry, University of Toronto, Toronto, ON, Canada. [e-mail].
Department of Immunology, University of Toronto, Toronto, ON, Canada. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B2C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A4B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 120.01 kDa 
• Atom Count: 8,061 
• Modeled Residue Count: 1,057 
• Deposited Residue Count: 1,105 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
52 Fab Heavy Chain	A [auth H]	220	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
52 Fab Light Chain	B [auth L]	215	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
298 Fab Light Chain	C [auth A]	220	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
298 Fab Heavy Chain	D [auth B]	222	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	E	228	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 (Subject of Investigation/LOI)	F [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free:  0.287 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.261 (Depositor), 0.263 (DCC) 
• R-Value Observed: 0.263 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.617	α = 90
b = 87.617	β = 90
c = 325.096	γ = 120

Software Package:

Software Name	Purpose
XPREP	data reduction
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-10-28 
Deposition Author(s): Newton, J.C., Kucharska, I., Rujas, E., Cui, H., Julien, J.P.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	6280100058
Canadian Institutes of Health Research (CIHR)	Canada	PJ4-169662

Revision History  

• Version 1.0: 2020-10-28
  Type: Initial release
  
• Version 1.1: 2021-01-27
  Changes: Structure summary
• Version 1.2: 2021-07-28
  Changes: Database references
• Version 1.3: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary