8CWJ

Fab arms of antibodies 4C12-B12 and CR3022 bound to pangolin receptor binding domain (pRBD)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.3 of the entry. See complete history


Literature

Affinity maturation endows potent activity onto class 6 SARS-CoV-2 broadly neutralizing antibodies.

Mazigi, O.Langley, D.B.Henry, J.Y.Burnett, D.L.Sobti, M.Walker, G.J.Rouet, R.Balachandran, H.Lenthall, H.Jackson, J.Ubiparipovic, S.Schofield, P.Brown, S.H.J.Schulz, S.R.Hoffmann, M.Pohlmann, S.Post, J.Martinello, M.Ahlenstiel, G.Kelleher, A.Rawlinson, W.D.Turville, S.G.Bull, R.A.Stewart, A.G.Jack, H.M.Goodnow, C.C.Christ, D.

(2025) Proc Natl Acad Sci U S A 122: e2417544121-e2417544121

  • DOI: https://doi.org/10.1073/pnas.2417544121
  • Primary Citation of Related Structures:  
    8CWI, 8CWJ, 8CWK

  • PubMed Abstract: 

    The emergence of SARS-CoV-2 variants of concern (VOCs) has greatly diminished the neutralizing activity of previously FDA-approved monoclonal antibodies (mAbs), including that of antibody cocktails and of first-generation broadly neutralizing antibodies such as S309 (Sotrovimab). In contrast, antibodies targeting cryptic conformational epitopes of the receptor binding domain (RBD) have demonstrated broad activity against emerging variants, but exert only moderate neutralizing activity, which has so far hindered clinical development. Here, we utilize in vitro display technology to identify and affinity-mature antibodies targeting the cryptic class 6 epitope, accessible only in the "up" conformation of the SARS-CoV-2 spike trimer. Increasing antibody affinity into the low picomolar range endowed potent neutralization of VOCs and protection of hACE2 mice from viral challenge. Cryoelectron microscopy and crystal structures of two affinity-matured antibodies (4C12-B12 and 4G1-C2) in complex with RBD highlighted binding modes and epitopes distal from mutational hotspots commonly overserved in VOCs, providing direct structural insights into the observed mutational resistance. Moreover, we further demonstrate that antibodies targeting the class 6 epitope, rather than being an artifact of in vitro selection, are common in the IgG1 + memory B cell repertoire of convalescent patients and can be induced in human antibody V-gene transgenic mice through immunization. Our results highlight the importance of very high (picomolar) affinity in the development of neutralizing antibodies and vaccines and suggest an affinity threshold in the provision of broad and long-lasting immunity against SARS-CoV-2.


  • Organizational Affiliation

    Garvan Institute of Medical Research, Sydney, NSW 2010, Australia.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heavy chain of CR3022 antibody FabA [auth H],
D [auth A]
230Homo sapiensMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Light chain of CR3022 antibody FabB [auth L],
E [auth B]
220Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoproteinC [auth G],
F [auth I]
204Pangolin coronavirusMutation(s): 0 
UniProt
Find proteins for A0A7D6PMV8 (Pangolin coronavirus)
Explore A0A7D6PMV8 
Go to UniProtKB:  A0A7D6PMV8
Entity Groups  
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UniProt GroupA0A7D6PMV8
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Heavy chain of 4C12-B12 antibody FabG [auth J],
I [auth U]
230Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Light chain of 4C12-B12 antibody FabH [auth K],
J [auth V]
215Homo 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-glucopyranoseK [auth C],
L [auth D],
M [auth E]
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

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

Download Ideal Coordinates CCD File 
DA [auth J]
EA [auth J]
GA [auth K]
IA [auth U]
KA [auth V]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth I]
BA [auth I]
CA [auth I]
FA [auth J]
HA [auth K]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.433α = 90
b = 144.097β = 117.51
c = 168.842γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-24
    Type: Initial release
  • Version 1.1: 2024-04-03
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-11-20
    Changes: Structure summary
  • Version 1.3: 2025-01-15
    Changes: Database references