8YK4 | pdb_00008yk4

Structure of SARS-CoV-2 RBD and antibody NT-108

• PDB DOI: https://doi.org/10.2210/pdb8YK4/pdb

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


• Deposited: 2024-03-04 Released: 2025-03-12 
• Deposition Author(s): Anraku, Y., Kita, S., Onodera, T., Sato, A., Tadokoro, T., Adachi, Y., Ito, S., Suzuki, T., Sasaki, J., Shiwa, N., Iwata, N., Nagata, N., Kazuki, Y., Oshimura, M., Sasaki, M., Orba, Y., Suzuki, T., Sawa, H., Hashiguchi, T., Fukuhara, H., Takahashi, Y., Maenaka, K.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.267 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.243 (Depositor), 0.245 (DCC) 
• R-Value Observed: 
  0.244 (Depositor) 

Starting Model: in silico

Literature

Structural Basis for Potent Neutralization Activity of SARS-CoV-2 Antibody, NT-108

Anraku, Y., Tadokoro, T., Suzuki, T., Sasaki, J., Hashiguchi, T., Kita, S., Shiwa, N., Iwata, N., Nagata, N., Suzuki, T., Kazuki, Y., Fukuhara, H., Oshimura, M., Sato, A., Sasaki, M., Orba, Y., Sawa, H., Maenaka, K.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 54.02 kDa 
• Atom Count: 3,179 
• Modelled Residue Count: 408 
• Deposited Residue Count: 497 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody NT-108, single chain Fv fragment	A	282	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	B [auth C]	215	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
UniProt
Find proteins for A0A7U3DZD0 (Severe acute respiratory syndrome coronavirus 2) Explore A0A7U3DZD0  Go to UniProtKB:  A0A7U3DZD0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.267 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.243 (Depositor), 0.245 (DCC) 
• R-Value Observed: 0.244 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.152	α = 90
b = 149.641	β = 90
c = 253.429	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-12 
Deposition Author(s): Anraku, Y., Kita, S., Onodera, T., Sato, A., Tadokoro, T., Adachi, Y., Ito, S., Suzuki, T., Sasaki, J., Shiwa, N., Iwata, N., Nagata, N., Kazuki, Y., Oshimura, M., Sasaki, M., Orba, Y., Suzuki, T., Sawa, H., Hashiguchi, T., Fukuhara, H., Takahashi, Y., Maenaka, K.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP20fk0108298
Japan Agency for Medical Research and Development (AMED)	Japan	JP20ae0101047
Japan Agency for Medical Research and Development (AMED)	Japan	JP20am0101093

Revision History  

• Version 1.0: 2025-03-12
  Type: Initial release