7YCO | pdb_00007yco

Crystal structure of SARS-CoV-2 Receptor Binding Domain bound to A6 repebody

• PDB DOI: https://doi.org/10.2210/pdb7YCO/pdb

• Classification: PROTEIN BINDING
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Cyclostomatida
• Expression System: Spodoptera frugiperda, Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-07-01 Released: 2023-07-05 
• Deposition Author(s): Kim, U.J., Cho, H.S.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 
  0.259 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.236 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

Literature

Crystal structure of SARS-CoV-2 Receptor Binding Domain bound to A6 repebody

Kim, U.J., Cho, H.S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 52.62 kDa 
• Atom Count: 3,757 
• Modeled Residue Count: 456 
• Deposited Residue Count: 465 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A	198	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
Repebody (A6)	B	267	Cyclostomatida	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free:  0.259 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.236 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.966	α = 90
b = 135.966	β = 90
c = 69.556	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-07-05 
Deposition Author(s): Kim, U.J., Cho, H.S.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2021R1A2C3010506
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2019M3E5D6063903

Revision History  

• Version 1.0: 2023-07-05
  Type: Initial release
  
• Version 1.1: 2024-10-09
  Changes: Data collection, Structure summary