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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.267 (Depositor), 0.236 (DCC)
R-Value Work:
0.243 (Depositor)
R-Value Observed:
0.244 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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| 3D Structure

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

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A7U3DZD0
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.267 (Depositor), 0.236 (DCC)
R-Value Work: 0.243 (Depositor)
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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-03-12

Deposition Author(s):

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