6XDG

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


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 

  • DOI: 10.1126/science.abd0827
  • Structures With Same Primary Citation

  • 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 ...

    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 SARS-CoV-2 spike protein, yielding a large collection of fully-human antibodies that were characterized for binding, neutralization and three dimensional structure. Based on these criteria, we selected pairs of highly-potent individual antibodies that simultaneously bind the receptor-binding domain of the spike protein, 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.


    Organizational Affiliation

    Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA. christos.kyratsous@regeneron.com.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Spike glycoprotein
E
251Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: S2
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Go to UniProtKB:  P0DTC2
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
REGN10933 antibody Fab fragment light chain
D
214Mus musculusMutation(s): 0 
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
REGN10933 antibody Fab fragment heavy chain
B
226Mus musculusMutation(s): 0 
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
REGN10987 antibody Fab fragment heavy chain
C
225Homo sapiensMutation(s): 0 
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
REGN10987 antibody Fab fragment light chain
A
216Homo sapiensMutation(s): 0 
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
E
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
BMA
Query on BMA

Download CCD File 
E
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
MAN
Query on MAN

Download CCD File 
E
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant 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