Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A3B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 123.52 kDa 
• Atom Count: 8004 
• Modelled Residue Count: 1043 
• Deposited Residue Count: 1132 
• Unique protein chains: 5

6XDG

Complex of SARS-CoV-2 receptor binding domain with the Fab fragments of two neutralizing antibodies

• PDB DOI: 10.2210/pdb6XDG/pdb
• EM Map EMD-22137:EMDBEMDataResource

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


• Deposited: 2020-06-10 Released: 2020-06-24 
• Deposition Author(s): Franklin, M.C., Saotome, K., Romero Hernandez, A., Zhou, Y.
• Funding Organization(s): Biomedical Advanced Research and Development Authority (BARDA)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Studies in humanized mice and convalescent humans yield a SARS-CoV-2 antibody cocktail.

Hansen, J., Baum, A., Pascal, K.E., Russo, V., Giordano, S., Wloga, E., Fulton, B.O., Yan, Y., Koon, K., Patel, K., Chung, K.M., Hermann, A., Ullman, E., Cruz, J., Rafique, A., Huang, T., Fairhurst, J., Libertiny, C., Malbec, M., Lee, W.Y., Welsh, R., Farr, G., Pennington, S., Deshpande, D., Cheng, J., Watty, A., Bouffard, P., Babb, R., Levenkova, N., Chen, C., Zhang, B., Romero Hernandez, A., Saotome, K., Zhou, Y., Franklin, M., Sivapalasingam, S., Lye, D.C., Weston, S., Logue, J., Haupt, R., Frieman, M., Chen, G., Olson, W., Murphy, A.J., Stahl, N., Yancopoulos, G.D., Kyratsous, C.A.

(2020) Science 369: 1010-1014

• PubMed: 32540901 
• DOI: 10.1126/science.abd0827
• Primary Citation of Related Structures:  
  6XDG


• PubMed Abstract: 
  

Neutralizing antibodies have become an important tool in treating infectious diseases. Recently, two separate approaches yielded successful antibody treatments for Ebola-one from genetically humanized mice and the other from a human survivor. Here, we describe parallel efforts using both humanized mice and convalescent patients to generate antibodies against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein, which yielded a large collection of fully human antibodies that were characterized for binding, neutralization, and three-dimensional structure. On the basis of these criteria, we selected pairs of highly potent individual antibodies that simultaneously bind the receptor binding domain of the spike protein, thereby providing ideal partners for a therapeutic antibody cocktail that aims to decrease the potential for virus escape mutants that might arise in response to selective pressure from a single-antibody treatment.

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Organizational Affiliation: 

Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A [auth E]	251	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
REGN10933 antibody Fab fragment light chain	B [auth D]	214	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
REGN10933 antibody Fab fragment heavy chain	C [auth B]	226	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
REGN10987 antibody Fab fragment heavy chain	D [auth C]	225	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
REGN10987 antibody Fab fragment light chain	E [auth A]	216	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 6
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22573RC GlyCosmos:  G22573RC GlyGen:  G22573RC

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2020-06-10 
• Released Date: 2020-06-24 
Deposition Author(s): Franklin, M.C., Saotome, K., Romero Hernandez, A., Zhou, Y.

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Funding Organization	Location	Grant Number
Biomedical Advanced Research and Development Authority (BARDA)		HHSO100201700020C

Revision History  

• Version 1.0: 2020-06-24
  Type: Initial release
  
• Version 1.1: 2020-07-08
  Changes: Author supporting evidence
• Version 1.2: 2020-07-22
  Changes: Source and taxonomy
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2020-09-02
  Changes: Database references, Structure summary
• Version 2.2: 2021-01-27
  Changes: Structure summary