7L7D

Crystal structure of SARS-CoV-2 spike RBD in complex with human monoclonal antibody AZD8895


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Genetic and structural basis for SARS-CoV-2 variant neutralization by a two-antibody cocktail.

Dong, J.Zost, S.J.Greaney, A.J.Starr, T.N.Dingens, A.S.Chen, E.C.Chen, R.E.Case, J.B.Sutton, R.E.Gilchuk, P.Rodriguez, J.Armstrong, E.Gainza, C.Nargi, R.S.Binshtein, E.Xie, X.Zhang, X.Shi, P.Y.Logue, J.Weston, S.McGrath, M.E.Frieman, M.B.Brady, T.Tuffy, K.M.Bright, H.Loo, Y.M.McTamney, P.M.Esser, M.T.Carnahan, R.H.Diamond, M.S.Bloom, J.D.Crowe Jr., J.E.

(2021) Nat Microbiol 6: 1233-1244

  • DOI: 10.1038/s41564-021-00972-2
  • Primary Citation of Related Structures:  
    7L7D, 7L7E

  • PubMed Abstract: 
  • Understanding the molecular basis for immune recognition of SARS-CoV-2 spike glycoprotein antigenic sites will inform the development of improved therapeutics. We determined the structures of two human monoclonal antibodies-AZD8895 and AZD1061-which form the basis of the investigational antibody cocktail AZD7442, in complex with the receptor-binding domain (RBD) of SARS-CoV-2 to define the genetic and structural basis of neutralization ...

    Understanding the molecular basis for immune recognition of SARS-CoV-2 spike glycoprotein antigenic sites will inform the development of improved therapeutics. We determined the structures of two human monoclonal antibodies-AZD8895 and AZD1061-which form the basis of the investigational antibody cocktail AZD7442, in complex with the receptor-binding domain (RBD) of SARS-CoV-2 to define the genetic and structural basis of neutralization. AZD8895 forms an 'aromatic cage' at the heavy/light chain interface using germ line-encoded residues in complementarity-determining regions (CDRs) 2 and 3 of the heavy chain and CDRs 1 and 3 of the light chain. These structural features explain why highly similar antibodies (public clonotypes) have been isolated from multiple individuals. AZD1061 has an unusually long LCDR1; the HCDR3 makes interactions with the opposite face of the RBD from that of AZD8895. Using deep mutational scanning and neutralization escape selection experiments, we comprehensively mapped the crucial binding residues of both antibodies and identified positions of concern with regards to virus escape from antibody-mediated neutralization. Both AZD8895 and AZD1061 have strong neutralizing activity against SARS-CoV-2 and variants of concern with antigenic substitutions in the RBD. We conclude that germ line-encoded antibody features enable recognition of the SARS-CoV-2 spike RBD and demonstrate the utility of the cocktail AZD7442 in neutralizing emerging variant viruses.


    Organizational Affiliation

    Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA. james.crowe@vumc.org.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
heavy chain of human monoclonal antibody Fab AZD8895A [auth H]226Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
light chain of human monoclonal antibody Fab AZD8895B [auth L]216Homo sapiensMutation(s): 0 
Entity Groups  
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Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Spike protein S1C [auth E]215Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: S2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
H [auth E]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth H],
E [auth H],
F [auth L],
G [auth L],
I [auth E],
D [auth H],
E [auth H],
F [auth L],
G [auth L],
I [auth E],
J [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.118α = 90
b = 81.583β = 94.6
c = 101.157γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

  • Deposited Date: 2020-12-28 
  • Released Date: 2021-09-01 
  • Deposition Author(s): Dong, J., Crowe, J.E.

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-01
    Type: Initial release
  • Version 1.1: 2022-03-16
    Changes: Database references