6XE1 | pdb_00006xe1

Structure of SARS-CoV-2 spike protein receptor binding domain in complex with a potent neutralizing antibody, CV30 Fab

• PDB DOI: https://doi.org/10.2210/pdb6XE1/pdb

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


• Deposited: 2020-06-11 Released: 2020-07-01 
• Deposition Author(s): Hurlburt, N.K., Pancera, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.239 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Models: experimental

Literature

Structural basis for potent neutralization of SARS-CoV-2 and role of antibody affinity maturation.

Hurlburt, N.K., Seydoux, E., Wan, Y.H., Edara, V.V., Stuart, A.B., Feng, J., Suthar, M.S., McGuire, A.T., Stamatatos, L., Pancera, M.

(2020) Nat Commun 11: 5413-5413

• PubMed: 33110068 
• DOI: https://doi.org/10.1038/s41467-020-19231-9
• Primary Citation Related Structures: 
  6XE1


• PubMed Abstract: 
  

  SARS-CoV-2 is a betacoronavirus virus responsible for the COVID-19 pandemic. Here, we determine the X-ray crystal structure of a potent neutralizing monoclonal antibody, CV30, isolated from a patient infected with SARS-CoV-2, in complex with the receptor binding domain. The structure reveals that CV30 binds to an epitope that overlaps with the human ACE2 receptor binding motif providing a structural basis for its neutralization. CV30 also induces shedding of the S1 subunit, indicating an additional mechanism of neutralization. A germline reversion of CV30 results in a substantial reduction in both binding affinity and neutralization potential indicating the minimal somatic mutation is needed for potently neutralizing antibodies against SARS-CoV-2.

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Organizational Affiliation: 
• Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA, USA.
Division of Infectious Disease, Department of Pediatrics, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University School of Medicine, Atlanta, GA, USA.
Department of Global Health, University of Washington, Seattle, WA, USA.
Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA, USA. [e-mail].
Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 77.69 kDa 
• Atom Count: 4,913 
• Modeled Residue Count: 638 
• Deposited Residue Count: 712 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CV30 Fab Heavy chain	A [auth H]	224	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CV30 Fab Kappa chain	B [auth L]	215	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	C [auth E]	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	D [auth E]	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 [auth H]	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.239 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.441	α = 90
b = 147.441	β = 90
c = 89.379	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-07-01 
Deposition Author(s): Hurlburt, N.K., Pancera, M.

Revision History  

• Version 1.0: 2020-07-01
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.2: 2022-04-13
  Changes: Database references, Structure summary
• Version 1.3: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.4: 2024-10-09
  Changes: Structure summary