8CBD

SARS-CoV-2 Delta-RBD complexed with BA.4/5-1 and EY6A Fabs

• PDB DOI: https://doi.org/10.2210/pdb8CBD/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2023-01-25 Released: 2024-02-07 
• Deposition Author(s): Zhou, D., Ren, J., Stuart, D.I.
• Funding Organization(s): CAMS Innovation Fund for Medical Sciences (CIFMS), Medical Research Council (MRC, United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.52 Å
• R-Value Free: 0.266 
• R-Value Work: 0.218 
• R-Value Observed: 0.220 

Literature

Potent cross-reactive mAbs from BA.4/5 breakthrough infection

Stuart, D.I.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A4B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: homology

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A4B1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A4B1 

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 352.24 kDa 
• Atom Count: 24,092 
• Modelled Residue Count: 3,147 
• Deposited Residue Count: 3,237 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A [auth R], J [auth X], M [auth Y]	202	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 2  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BA.4/5-1 heavy chain	B [auth H], K [auth A], N [auth C]	222	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
BA.4/5-1 light chain	C [auth L], L [auth B], O [auth D]	214	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
EY6A heavy chain	D [auth E], F [auth G], H [auth J]	226	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
EY6A light chain	E [auth F], G [auth I], I [auth K]	215	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	P [auth R]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.52 Å
• R-Value Free: 0.266 
• R-Value Work: 0.218 
• R-Value Observed: 0.220 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 242.046	α = 90
b = 139.369	β = 115.58
c = 168.528	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
GDA	data collection
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-07 
Deposition Author(s): Zhou, D., Ren, J., Stuart, D.I.

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Funding Organization	Location	Grant Number
CAMS Innovation Fund for Medical Sciences (CIFMS)	United Kingdom	2018-I2M-2-002
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/N00065X/1

Revision History  

• Version 1.0: 2024-02-07
  Type: Initial release