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- PDB-7ycl: Crystal structure of SARS-CoV-2 Spike RBD in complex with IS-9A Fab -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ycl | ||||||
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Title | Crystal structure of SARS-CoV-2 Spike RBD in complex with IS-9A Fab | ||||||
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![]() | VIRAL PROTEIN/IMMUNE SYSTEM / antibody / SARS-CoV-2 / Spike / RBD / class 4 / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
Function / homology | ![]() Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mohapatra, A. / Chen, X. | ||||||
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![]() | ![]() Title: Structural basis for a conserved neutralization epitope on the receptor-binding domain of SARS-CoV-2. Authors: Kuan-Ying A Huang / Xiaorui Chen / Arpita Mohapatra / Hong Thuy Vy Nguyen / Lisa Schimanski / Tiong Kit Tan / Pramila Rijal / Susan K Vester / Rory A Hills / Mark Howarth / Jennifer R Keeffe ...Authors: Kuan-Ying A Huang / Xiaorui Chen / Arpita Mohapatra / Hong Thuy Vy Nguyen / Lisa Schimanski / Tiong Kit Tan / Pramila Rijal / Susan K Vester / Rory A Hills / Mark Howarth / Jennifer R Keeffe / Alexander A Cohen / Leesa M Kakutani / Yi-Min Wu / Md Shahed-Al-Mahmud / Yu-Chi Chou / Pamela J Bjorkman / Alain R Townsend / Che Ma / ![]() ![]() ![]() 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 ...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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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 281.9 KB | Display | ![]() |
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PDB format | ![]() | 220.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 778.3 KB | Display | ![]() |
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Full document | ![]() | 789.9 KB | Display | |
Data in XML | ![]() | 56.8 KB | Display | |
Data in CIF | ![]() | 84.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7yckC ![]() 7ycnC ![]() 8hhxC ![]() 8hhyC ![]() 8hhzC ![]() 6zerS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Assembly
Deposited unit | ![]()
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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