7MSQ | pdb_00007msq

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

• PDB DOI: https://doi.org/10.2210/pdb7MSQ/pdb

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


• Deposited: 2021-05-12 Released: 2022-01-19 
• Deposition Author(s): Langley, D.B., Christ, D.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 
  0.245 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.194 (Depositor) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Models: experimental

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

• PubMed: 34788600 
• DOI: https://doi.org/10.1016/j.immuni.2021.10.019
• Primary Citation 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.

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Organizational Affiliation: 
• Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; UNSW Sydney, Faculty of Medicine, Sydney, NSW 2010, Australia. Electronic address: [e-mail].
Garvan Institute of Medical Research, Sydney, NSW 2010, Australia.
Kirby Institute, UNSW, Sydney, NSW 2052, Australia.
Center for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW 2006, Australia.
Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; UNSW Sydney, Faculty of Medicine, Sydney, NSW 2010, Australia.
UNSW Sydney, Faculty of Medicine, Sydney, NSW 2010, Australia.
UNSW Sydney, Faculty of Medicine, Sydney, NSW 2010, Australia; Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia.
Division of Molecular Immunology, University Hospital Erlangen, University of Erlangen-Nürnberg, Erlangen 91054, Germany.
Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
Centenary Institute, The University of Sydney, Sydney, NSW 2006, Australia.
UNSW Sydney, Faculty of Medicine, Sydney, NSW 2010, Australia; Serology and Virology Division (SAViD), NSW Health Pathology, SEALS Randwick, Sydney, NSW 2031, Australia.
Division of Genetics, Department Biology, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Erlangen 91054, Germany.
UNSW Sydney, Faculty of Medicine, Sydney, NSW 2010, Australia; Kirby Institute, UNSW, Sydney, NSW 2052, Australia.
Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; Cellular Genomics Futures Institute, UNSW Sydney, Sydney, NSW 2052, Australia.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 145.71 kDa 
• Atom Count: 9,962 
• Modeled Residue Count: 1,253 
• Deposited Residue Count: 1,312 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A, B	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
AB-3467 Fab Heavy Chain	C [auth D], E [auth H]	238	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
AB-3467 Fab Light Chain	D [auth E], F [auth L]	214	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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-glucopyranose	G [auth C]	5		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42466VF GlyCosmos: G42466VF GlyGen: G42466VF

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	M [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
SCN	J [auth B], P [auth E], R [auth L], S [auth L], T [auth L]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M
CL	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 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.194 (Depositor) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.764	α = 90
b = 115.494	β = 90
c = 240.758	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-01-19 
Deposition Author(s): Langley, D.B., Christ, D.

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

Revision History  

• 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