8OWV

H6 and F2 nanobodies bound to SARS-CoV-2 spike RBD

• PDB DOI: https://doi.org/10.2210/pdb8OWV/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Lama glama
• Expression System: Homo sapiens, Escherichia coli
• Mutation(s): No 


• Deposited: 2023-04-28 Released: 2024-05-08 
• Deposition Author(s): Mikolajek, H., Naismith, J.H., Owens, R.J.
• Funding Organization(s): Wellcome Trust

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.223 
• R-Value Work: 0.197 

Literature

Trimeric nanobodies potently neutralize Omicron variants of SARS-CoV-2

Cornish, K.A.S., Mikolajek, H., Naismith, J.H., Owens, R.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 53.69 kDa 
• Atom Count: 3,782 
• Modelled Residue Count: 449 
• Deposited Residue Count: 474 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A [auth EEE]	209	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
UniProt
Find proteins for A0A8A5XRG7 (Severe acute respiratory syndrome coronavirus 2) Explore A0A8A5XRG7  Go to UniProtKB:  A0A8A5XRG7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
F2	B [auth BBB]	132	Lama glama	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
H6	C [auth FFF]	133	Lama glama	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth EEE]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	E [auth EEE], F [auth EEE], G [auth BBB]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.223 
• R-Value Work: 0.197 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.775	α = 90
b = 59.438	β = 90
c = 145.624	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
DIALS	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-08 
Deposition Author(s): Mikolajek, H., Naismith, J.H., Owens, R.J.

---

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	223733/Z/21/Z

Revision History  

• Version 1.0: 2024-05-08
  Type: Initial release