7MSQ

Complex between the Fab arm of AB-3467 and the SARS-CoV-2 receptor binding domain (RBD)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Immunizations with diverse sarbecovirus receptor-binding domains elicit SARS-CoV-2 neutralizing antibodies against a conserved site of vulnerability.

Burnett, D.L.Jackson, K.J.L.Langley, D.B.Aggrawal, A.Stella, A.O.Johansen, M.D.Balachandran, H.Lenthall, H.Rouet, R.Walker, G.Saunders, B.M.Singh, M.Li, H.Henry, J.Y.Jackson, J.Stewart, A.G.Witthauer, F.Spence, M.A.Hansbro, N.G.Jackson, C.Schofield, P.Milthorpe, C.Martinello, M.Schulz, S.R.Roth, E.Kelleher, A.Emery, S.Britton, W.J.Rawlinson, W.D.Karl, R.Schafer, S.Winkler, T.H.Brink, R.Bull, R.A.Hansbro, P.M.Jack, H.M.Turville, S.Christ, D.Goodnow, C.C.

(2021) Immunity 54: 2908-2921.e6

  • DOI: https://doi.org/10.1016/j.immuni.2021.10.019
  • Primary Citation of Related Structures:  
    7MSQ

  • PubMed Abstract: 

    Viral mutations are an emerging concern in reducing SARS-CoV-2 vaccination efficacy. Second-generation vaccines will need to elicit neutralizing antibodies against sites that are evolutionarily conserved across the sarbecovirus subgenus. Here, we immunized mice containing a human antibody repertoire with diverse sarbecovirus receptor-binding domains (RBDs) to identify antibodies targeting conserved sites of vulnerability. Antibodies with broad reactivity against diverse clade B RBDs targeting the conserved class 4 epitope, with recurring IGHV/IGKV pairs, were readily elicited but were non-neutralizing. However, rare class 4 antibodies binding this conserved RBD supersite showed potent neutralization of SARS-CoV-2 and all variants of concern. Structural analysis revealed that the neutralizing ability of cross-reactive antibodies was reserved only for those with an elongated CDRH3 that extends the antiparallel beta-sheet RBD core and orients the antibody light chain to obstruct ACE2-RBD interactions. These results identify a structurally defined pathway for vaccine strategies eliciting escape-resistant SARS-CoV-2 neutralizing antibodies.


  • Organizational Affiliation

    Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; UNSW Sydney, Faculty of Medicine, Sydney, NSW 2010, Australia. Electronic address: d.burnett@garvan.org.au.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike protein S1
A, B
204Severe 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
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P0DTC2-1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
AB-3467 Fab Heavy ChainC [auth D],
E [auth H]
238Homo sapiensMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
AB-3467 Fab Light ChainD [auth E],
F [auth L]
214Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth C]5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42466VF
GlyCosmos:  G42466VF
GlyGen:  G42466VF
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
M [auth D]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
SCN
Query on SCN

Download Ideal Coordinates CCD File 
J [auth B],
P [auth E],
R [auth L],
S [auth L],
T [auth L]
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth A]
I [auth B]
K [auth D]
L [auth D]
N [auth E]
H [auth A],
I [auth B],
K [auth D],
L [auth D],
N [auth E],
O [auth E],
Q [auth H]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.764α = 90
b = 115.494β = 90
c = 240.758γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



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: 2022-01-19
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-23
    Changes: Structure summary