7M3I | pdb_00007m3i

Structure of SARS-CoV-2 spike protein receptor binding domain in complex with a neutralizing antibody, CV2-75 Fab

• PDB DOI: https://doi.org/10.2210/pdb7M3I/pdb

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


• Deposited: 2021-03-18 Released: 2021-05-12 
• Deposition Author(s): Hurlburt, N.K., Pancera, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.281 (Depositor), 0.285 (DCC) 
• R-Value Work: 
  0.245 (Depositor), 0.249 (DCC) 
• R-Value Observed: 
  0.247 (Depositor) 

Starting Models: experimental

Literature

Isolation and characterization of cross-neutralizing coronavirus antibodies from COVID-19+ subjects.

Jennewein, M.F., MacCamy, A.J., Akins, N.R., Feng, J., Homad, L.J., Hurlburt, N.K., Seydoux, E., Wan, Y.H., Stuart, A.B., Edara, V.V., Floyd, K., Vanderheiden, A., Mascola, J.R., Doria-Rose, N., Wang, L., Yang, E.S., Chu, H.Y., Torres, J.L., Ozorowski, G., Ward, A.B., Whaley, R.E., Cohen, K.W., Pancera, M., McElrath, M.J., Englund, J.A., Finzi, A., Suthar, M.S., McGuire, A.T., Stamatatos, L.

(2021) Cell Rep 36: 109353-109353

• PubMed: 34237283 
• DOI: https://doi.org/10.1016/j.celrep.2021.109353
• Primary Citation Related Structures: 
  7M3I


• PubMed Abstract: 
  

  SARS-CoV-2 is one of three coronaviruses that have crossed the animal-to-human barrier and caused widespread disease in the past two decades. The development of a universal human coronavirus vaccine could prevent future pandemics. We characterize 198 antibodies isolated from four COVID-19+ subjects and identify 14 SARS-CoV-2 neutralizing antibodies. One targets the N-terminal domain (NTD), one recognizes an epitope in S2, and 11 bind the receptor-binding domain (RBD). Three anti-RBD neutralizing antibodies cross-neutralize SARS-CoV-1 by effectively blocking binding of both the SARS-CoV-1 and SARS-CoV-2 RBDs to the ACE2 receptor. Using the K18-hACE transgenic mouse model, we demonstrate that the neutralization potency and antibody epitope specificity regulates the in vivo protective potential of anti-SARS-CoV-2 antibodies. All four cross-neutralizing antibodies neutralize the B.1.351 mutant strain. Thus, our study reveals that epitopes in S2 can serve as blueprints for the design of immunogens capable of eliciting cross-neutralizing coronavirus antibodies.

---

Organizational Affiliation: 
• Fred Hutchinson Cancer Research Center, Vaccines and Infectious Disease Division, Seattle, WA 98109, USA.
Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30322, USA.
Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA.
University of Washington, Department of Medicine, Seattle, WA 98109, USA.
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
Fred Hutchinson Cancer Research Center, Vaccines and Infectious Disease Division, Seattle, WA 98109, USA; Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA.
Fred Hutchinson Cancer Research Center, Vaccines and Infectious Disease Division, Seattle, WA 98109, USA; University of Washington, Department of Medicine, Seattle, WA 98109, USA; University of Washington, Department of Global Health, Seattle, WA 98109, USA.
Department of Pediatrics, University of Washington and Seattle Children's Research Institute, Seattle, WA 98109, USA.
Université de Montréal, Montreal, QC, Canada.
Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30322, USA. Electronic address: [e-mail].
Fred Hutchinson Cancer Research Center, Vaccines and Infectious Disease Division, Seattle, WA 98109, USA; University of Washington, Department of Global Health, Seattle, WA 98109, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA. Electronic address: [e-mail].
Fred Hutchinson Cancer Research Center, Vaccines and Infectious Disease Division, Seattle, WA 98109, USA; University of Washington, Department of Global Health, Seattle, WA 98109, USA. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 155.68 kDa 
• Atom Count: 9,872 
• Modeled Residue Count: 1,282 
• Deposited Residue Count: 1,428 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CV2-75 Fab Heavy chain	A, D [auth H]	227	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CV2-75 Fab Light chain	B, E [auth L]	214	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	C, F [auth R]	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: 1		Go to GlyGen: P0DTC2-1

Small Molecules

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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A, D [auth H]	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.281 (Depositor), 0.285 (DCC) 
• R-Value Work:  0.245 (Depositor), 0.249 (DCC) 
• R-Value Observed: 0.247 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.371	α = 90
b = 127.519	β = 90
c = 155.672	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-05-12 
Deposition Author(s): Hurlburt, N.K., Pancera, M.

Revision History  

• Version 1.0: 2021-05-12
  Type: Initial release
  
• Version 1.1: 2021-07-28
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary