8SIS

Crystal structure of SARS-CoV-2 spike receptor-binding domain in complex with broadly neutralizing antibody CC84.2 Fab

• PDB DOI: https://doi.org/10.2210/pdb8SIS/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
• Expression System: Trichoplusia ni, Mus musculus
• Mutation(s): No 


• Deposited: 2023-04-16 Released: 2024-03-13 
• Deposition Author(s): Liu, H., Wilson, I.A.
• Funding Organization(s): Bill & Melinda Gates Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.08 Å
• R-Value Free: 0.303 
• R-Value Work: 0.256 
• R-Value Observed: 0.258 

Literature

Broadly neutralizing antibodies targeting a conserved silent face of spike RBD resist extreme SARS-CoV-2 antigenic drift

Song, G., Yuan, M., Liu, H., Capozzola, T., Lin, R., Torres, J., He, W., Musharrafieh, R., Dueker, K., Zhou, P., Callaghan, S., Mishra, N., Yong, P., Anzanello, F., Avillion, G., Vo, A., Li, X., Makhdoomi, M., Feng, Z., Zhu, X., Peng, L., Nemazee, D., Safonova, Y., Briney, B., Ward, A., Burton, D., Wilson, I., Andrabi, R.

(2023) Biorxiv 

• DOI: https://doi.org/10.1101/2023.04.26.538488

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 71.86 kDa 
• Atom Count: 4,647 
• Modelled Residue Count: 632 
• Deposited Residue Count: 652 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A	205	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
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
CC84.2 Fab heavy chain	B [auth H]	231	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CC84.2 Fab light chain	C [auth L]	216	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [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: 3.08 Å
• R-Value Free: 0.303 
• R-Value Work: 0.256 
• R-Value Observed: 0.258 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.698	α = 90
b = 80.188	β = 94.9
c = 73.537	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-13 
Deposition Author(s): Liu, H., Wilson, I.A.

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Funding Organization	Location	Grant Number
Bill & Melinda Gates Foundation	United States	INV-004923

Revision History  

• Version 1.0: 2024-03-13
  Type: Initial release