7KZA

Potent SARS-CoV-2 binding and neutralization through maturation of iconic SARS-CoV-1antibodies


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Potent SARS-CoV-2 binding and neutralization through maturation of iconic SARS-CoV-1 antibodies.

Rouet, R.Mazigi, O.Walker, G.J.Langley, D.B.Sobti, M.Schofield, P.Lenthall, H.Jackson, J.Ubiparipovic, S.Henry, J.Y.Abayasingam, A.Burnett, D.Kelleher, A.Brink, R.Bull, R.A.Turville, S.Stewart, A.G.Goodnow, C.C.Rawlinson, W.D.Christ, D.

(null) MAbs 13: 1922134-1922134

  • DOI: https://doi.org/10.1080/19420862.2021.1922134
  • Primary Citation of Related Structures:  
    7KZA, 7KZB, 7KZC

  • PubMed Abstract: 

    Antibodies against coronavirus spike protein potently protect against infection and disease, but whether such protection can be extended to variant coronaviruses is unclear. This is exemplified by a set of iconic and well-characterized monoclonal antibodies developed after the 2003 SARS outbreak, including mAbs m396, CR3022, CR3014 and 80R, which potently neutralize SARS-CoV-1, but not SARS-CoV-2. Here, we explore antibody engineering strategies to change and broaden their specificity, enabling nanomolar binding and potent neutralization of SARS-CoV-2. Intriguingly, while many of the matured clones maintained specificity of the parental antibody, new specificities were also observed, which was further confirmed by X-ray crystallography and cryo-electron microscopy, indicating that a limited set of VH antibody domains can give rise to variants targeting diverse epitopes, when paired with a diverse VL repertoire. Our findings open up over 15 years of antibody development efforts against SARS-CoV-1 to the SARS-CoV-2 field and outline general principles for the maturation of antibody specificity against emerging viruses.


  • Organizational Affiliation

    Immunology Department, Garvan Institute of Medical Research, Sydney, NSW, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fab fragment heavy chain of anti-CoV2-RBD antibody variant CR3022-B6A [auth H]230Homo sapiensMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab fragment light chain of anti-CoV2-RBD antibody variant CR3022-B6B [auth L]214Homo sapiensMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
K [auth L]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth H],
E [auth H],
F [auth H],
I [auth L],
J [auth L]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth H],
G [auth L]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
H [auth L]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.749α = 90
b = 70.749β = 90
c = 249.52γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-24
    Type: Initial release
  • Version 1.1: 2021-06-09
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Advisory, Data collection, Database references, Refinement description