8YUB | pdb_00008yub

Crystal structure of SARS-CoV-2 ConSp RBD in complex with neutralizing antibody CC25.4 Fab

• PDB DOI: https://doi.org/10.2210/pdb8YUB/pdb

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


• Deposited: 2024-03-27 Released: 2025-10-01 
• Deposition Author(s): Kang, J.M., Yuan, M., Han, B.W., Wilson, I.A.
• Funding Organization(s): Bill & Melinda Gates Foundation, National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 
  0.255 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Structure and antigenic characteristics of consensus sequence-based SARS-CoV-2 antigen

Kang, J.M., Yuan, M., Han, B.W., Wilson, I.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 140.88 kDa 
• Atom Count: 10,211 
• Modeled Residue Count: 1,284 
• Deposited Residue Count: 1,284 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neutralizing antibody CC25.4 heavy chain	A, D	228	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Neutralizing antibody CC25.4 light chain	B, E	217	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S2'	C, F	197	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 24  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

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, H	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC GlyCosmos:  G86851RC GlyGen:  G86851RC

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	I [auth B], J [auth E]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free:  0.255 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.352	α = 90
b = 124.901	β = 104.37
c = 85.74	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
HKL-2000	data collection
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-01 
Deposition Author(s): Kang, J.M., Yuan, M., Han, B.W., Wilson, I.A.

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Funding Organization	Location	Grant Number
Bill & Melinda Gates Foundation	United States	INV-004923
National Research Foundation (NRF, Korea)	Korea, Republic Of	2019R1A2C1090251
National Research Foundation (NRF, Korea)	Korea, Republic Of	RS-2023-00218543

Revision History  

• Version 1.0: 2025-10-01
  Type: Initial release