7YCK | pdb_00007yck

Crystal structure of SARS-CoV-2 Spike RBD in complex with FP-12A Fab

• PDB DOI: https://doi.org/10.2210/pdb7YCK/pdb

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


• Deposited: 2022-07-01 Released: 2023-02-01 
• Deposition Author(s): Nguyen, V.H.T., Chen, X.
• Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.264 (Depositor) 
• R-Value Work: 
  0.229 (Depositor) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

Literature

Structural basis for a conserved neutralization epitope on the receptor-binding domain of SARS-CoV-2.

Huang, K.A., Chen, X., Mohapatra, A., Nguyen, H.T.V., Schimanski, L., Tan, T.K., Rijal, P., Vester, S.K., Hills, R.A., Howarth, M., Keeffe, J.R., Cohen, A.A., Kakutani, L.M., Wu, Y.M., Shahed-Al-Mahmud, M., Chou, Y.C., Bjorkman, P.J., Townsend, A.R., Ma, C.

(2023) Nat Commun 14: 311-311

• PubMed: 36658148 
• DOI: https://doi.org/10.1038/s41467-023-35949-8
• Primary Citation Related Structures: 
  7YCK, 7YCL, 7YCN, 8HHX, 8HHY, 8HHZ


• PubMed Abstract: 
  

  Antibody-mediated immunity plays a crucial role in protection against SARS-CoV-2 infection. We isolated a panel of neutralizing anti-receptor-binding domain (RBD) antibodies elicited upon natural infection and vaccination and showed that they recognize an immunogenic patch on the internal surface of the core RBD, which faces inwards and is hidden in the "down" state. These antibodies broadly neutralize wild type (Wuhan-Hu-1) SARS-CoV-2, Beta and Delta variants and some are effective against other sarbecoviruses. We observed a continuum of partially overlapping antibody epitopes from lower to upper part of the inner face of the RBD and some antibodies extend towards the receptor-binding motif. The majority of antibodies are substantially compromised by three mutational hotspots (S371L/F, S373P and S375F) in the lower part of the Omicron BA.1, BA.2 and BA.4/5 RBD. By contrast, antibody IY-2A induces a partial unfolding of this variable region and interacts with a conserved conformational epitope to tolerate all antigenic variations and neutralize diverse sarbecoviruses as well. This finding establishes that antibody recognition is not limited to the normal surface structures on the RBD. In conclusion, the delineation of functionally and structurally conserved RBD epitopes highlights potential vaccine and therapeutic candidates for COVID-19.

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Organizational Affiliation: 
• Graduate Institute of Immunology and Department of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan. [e-mail].
Genomics Research Center, Academia Sinica, Taipei, Taiwan. [e-mail].
College of Medicine, Chang Gung University, Taoyuan, Taiwan. [e-mail].
Genomics Research Center, Academia Sinica, Taipei, Taiwan.
Chemical Biology and Molecular Biophysics program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan.
Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan.
MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK.
Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK.
Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA.
Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.
Biomedical Translation Research Center, Academia Sinica, Taipei, 11529, Taiwan.
Genomics Research Center, Academia Sinica, Taipei, Taiwan. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 141.5 kDa 
• Atom Count: 8,315 
• Modeled Residue Count: 1,053 
• Deposited Residue Count: 1,288 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A, D [auth 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
FP-12A Fab heavy chain	B [auth C], E	224	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
FP-12A Fab light chain	C [auth D], F	216	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
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	4		N-Glycosylation
Glycosylation Resources
GlyTouCan: G32152BH GlyCosmos: G32152BH GlyGen: G32152BH

Entity ID: 5
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	H	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.264 (Depositor) 
• R-Value Work:  0.229 (Depositor) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.83	α = 76.26
b = 79.124	β = 81.16
c = 92.539	γ = 71.13

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-02-01 
Deposition Author(s): Nguyen, V.H.T., Chen, X.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	--

Revision History  

• Version 1.0: 2023-02-01
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-09
  Changes: Structure summary