7KZB

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free: 0.336 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.256 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.2 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fab heavy chain of CR3014-C8 antibodyA [auth H]231Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab light chain of CR3014-C8 antibodyB [auth L]214Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein204Severe 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  
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UniProt GroupP0DTC2
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P0DTC2-1
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Fab heavy chain of CR3022-B6 antibodyD [auth A]230Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Fab light chain of CR3022-B6 antibodyE [auth B]214Homo sapiensMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

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Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseF [auth D]3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth L]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free: 0.336 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.256 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.183α = 90
b = 147.674β = 90
c = 157.199γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-03
    Type: Initial release
  • Version 2.0: 2021-06-09
    Type: Coordinate replacement
    Reason: Chirality error
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 2.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description
  • Version 2.2: 2024-11-06
    Changes: Structure summary