8SIQ

Crystal structure of SARS-CoV-2 spike receptor-binding domain in complex with broadly neutralizing antibodies CC25.36 and CV38-142 Fab

• PDB DOI: https://doi.org/10.2210/pdb8SIQ/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: 2.50 Å
• R-Value Free: 0.287 
• R-Value Work: 0.247 
• R-Value Observed: 0.249 

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 5-mer - A1B1C1D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A4B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 118.88 kDa 
• Atom Count: 7,963 
• Modelled Residue Count: 1,064 
• Deposited Residue Count: 1,095 
• Unique protein chains: 5

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
CC25.36 Fab heavy chain	B [auth H]	230	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CC25.36 Fab light chain	C [auth L]	217	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
CV38-142 Fab heavy chain	D [auth M]	226	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
CV38-142 Fab light chain	E [auth N]	217	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth B]	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G32152BH GlyCosmos:  G32152BH GlyGen:  G32152BH

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.287 
• R-Value Work: 0.247 
• R-Value Observed: 0.249 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.399	α = 90
b = 77.035	β = 90
c = 266.445	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