8K5G

Structure of the SARS-CoV-2 BA.1 RBD with UT28-RD

• PDB DOI: https://doi.org/10.2210/pdb8K5G/pdb
• EM Map EMD-36905: EMDB EMDataResource

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2023-07-21 Released: 2023-12-27 
• Deposition Author(s): Chen, L., Kita, S., Anraku, Y., Maenaka, K.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Japan Society for the Promotion of Science (JSPS), Other government

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.41 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

In silico-designed UT28K with two amino acid substitutions is capable of neutralization of resistant SARS-CoV2 Omicrons BA.1 valiant.

Ozawa, T., Ikeda, Y., Chen, L., Suzuki, R., Hoshino, A., Noguchi, A., Kita, S., Anraku, Y., Igarashi, E., Saga, Y., Inasaki, N., Taminishi, S., Sasaki, J., Kirita, Y., Fukuhara, H., Maenaka, K., Hashiguchi, T., Fukuhara, T., Hirabayashi, K., Tani, H., Kishi, H., Niimi, H.

To be published.

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.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 78.37 kDa 
• Atom Count: 3,381 
• Modelled Residue Count: 431 
• Deposited Residue Count: 712 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UT28K-RD Fab Heavy chain	A [auth H]	252	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
UT28K-RD Fab Light chain	B [auth L]	235	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	C [auth A]	225	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 16  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.41 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1
RECONSTRUCTION	cryoSPARC	3.3.1

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-27 
Deposition Author(s): Chen, L., Kita, S., Anraku, Y., Maenaka, K.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP21am0101077 and JP22ama121010
Japan Agency for Medical Research and Development (AMED)	Japan	JP22ae0121018
Japan Society for the Promotion of Science (JSPS)	Japan	JP20K07624 and JP23H02776
Japan Agency for Medical Research and Development (AMED)	Japan	JP23fa627009
Other government		JPMJCR20H8

Revision History  

• Version 1.0: 2023-12-27
  Type: Initial release