8DXT | pdb_00008dxt

Fab arm of antibody GAR12 bound to the receptor binding domain of SARS-CoV-2.

• PDB DOI: https://doi.org/10.2210/pdb8DXT/pdb

• Classification: ANTIVIRAL PROTEIN
• Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2022-08-03 Released: 2023-01-18 
• Deposition Author(s): Langley, D.B., Christ, D., Henry, J.Y.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.254 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

Broadly neutralizing SARS-CoV-2 antibodies through epitope-based selection from convalescent patients.

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

(2023) Nat Commun 14: 687-687

• PubMed: 36755042 
• DOI: https://doi.org/10.1038/s41467-023-36295-5
• Primary Citation Related Structures: 
  7T5O, 7T72, 8DXT, 8DXU


• PubMed Abstract: 
  

  Emerging variants of concern (VOCs) are threatening to limit the effectiveness of SARS-CoV-2 monoclonal antibodies and vaccines currently used in clinical practice; broadly neutralizing antibodies and strategies for their identification are therefore urgently required. Here we demonstrate that broadly neutralizing antibodies can be isolated from peripheral blood mononuclear cells of convalescent patients using SARS-CoV-2 receptor binding domains carrying epitope-specific mutations. This is exemplified by two human antibodies, GAR05, binding to epitope class 1, and GAR12, binding to a new epitope class 6 (located between class 3 and 5). Both antibodies broadly neutralize VOCs, exceeding the potency of the clinical monoclonal sotrovimab (S309) by orders of magnitude. They also provide prophylactic and therapeutic in vivo protection of female hACE2 mice against viral challenge. Our results indicate that exposure to SARS-CoV-2 induces antibodies that maintain broad neutralization against emerging VOCs using two unique strategies: either by targeting the divergent class 1 epitope in a manner resistant to VOCs (ACE2 mimicry, as illustrated by GAR05 and mAbs P2C-1F11/S2K14); or alternatively, by targeting rare and highly conserved epitopes, such as the new class 6 epitope identified here (as illustrated by GAR12). Our results provide guidance for next generation monoclonal antibody development and vaccine design.

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Organizational Affiliation: 
• Garvan Institute of Medical Research, Sydney, NSW, Australia. [e-mail].
UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia. [e-mail].
Garvan Institute of Medical Research, Sydney, NSW, Australia.
UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia.
Center for Inflammation, Centenary Institute and University of Technology Sydney, Sydney, NSW, Australia.
Victor Chang Cardiac Research Institute, Sydney, NSW, Australia.
UNSW Sydney, School of Medical Sciences, Faculty of Medicine, Sydney, NSW, Australia.
Kirby Institute, UNSW Sydney, Sydney, NSW, Australia.
Prince of Wales Hospital, Sydney, NSW, Australia.
Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia.
Royal North Shore Hospital, Sydney, NSW, Australia.
Westmead Hospital, Sydney, NSW, Australia.
Division of Molecular Immunology, Friedrich-Alexander University Erlangen-Nürnberg and University Hospital Erlangen, Erlangen-Nürnberg, Germany.
Garvan Institute of Medical Research, Sydney, NSW, Australia. [e-mail].
UNSW Sydney, St Vincent's Clinical School, Faculty of Medicine, Sydney, NSW, Australia. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 71.66 kDa 
• Atom Count: 4,857 
• Modeled Residue Count: 622 
• Deposited Residue Count: 652 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of Fab arm of antibody GAR12	A [auth L]	214	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of Fab arm of antibody GAR12	B [auth H]	234	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	C [auth R]	204	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P0DTC2-1

Oligosaccharides

Help  

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth A]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.254 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.609	α = 90
b = 41.954	β = 97.08
c = 183.029	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-01-18 
Deposition Author(s): Langley, D.B., Christ, D., Henry, J.Y.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	--

Revision History  

• Version 1.0: 2023-01-18
  Type: Initial release
  
• Version 1.1: 2023-02-22
  Changes: Database references
• Version 1.2: 2023-10-25
  Changes: Data collection, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary