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)

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
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wwPDB Validation 3D Report Full Report

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

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.

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

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| 3D Structure

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

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| 3D Structure

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

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTC2
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain C Focus chain F	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain J [auth E] SDF format, chain I [auth B] MOL2 format, chain J [auth E] MOL2 format, chain I [auth B] mmCIF format, chain J [auth E] mmCIF format, chain I [auth B]	I [auth B], J [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain J [auth E] Interactions & Density Focus chain I [auth B] Focus chain J [auth E]

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

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-10-01

Deposition Author(s):

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