8RBY

The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the neutralizing nanobody 1.26

• PDB DOI: https://doi.org/10.2210/pdb8RBY/pdb

• Classification: ANTIVIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Camelus dromedarius
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2023-12-05 Released: 2024-12-11 
• Deposition Author(s): Casasnovas, J.M., Fernandez, L.A., Silva, K.
• Funding Organization(s): Ministerio de Ciencia e Innovacion (MCIN)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.234 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 

Starting Models: experimental

Literature

The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the neutralizing nanobody 1.26

Casasnovas, J.M., Fernandez, L.A., Silva, K.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: surface plasmon resonance

Macromolecule Content

• Total Structure Weight: 36.38 kDa 
• Atom Count: 2,726 
• Modelled Residue Count: 316 
• Deposited Residue Count: 326 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A	203	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Camel-derived nanobody 1.26	B	123	Camelus dromedarius	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MPO	D [auth A]	3[N-MORPHOLINO]PROPANE SULFONIC ACID C7 H15 N O4 S DVLFYONBTKHTER-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.234 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.481	α = 90
b = 55.915	β = 104.31
c = 58.774	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-11 
Deposition Author(s): Casasnovas, J.M., Fernandez, L.A., Silva, K.

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Funding Organization	Location	Grant Number
Ministerio de Ciencia e Innovacion (MCIN)	Spain	202020E079

Revision History  

• Version 1.0: 2024-12-11
  Type: Initial release